Papers Citing TimeLogic® Products
The following articles reference the use of TimeLogic's DeCypher® and CodeQuest® bioinformatics systems. Click on the links to view abstracts or full text where available.
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Prediction of the protein components of a putative Calanus finmarchicus (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome.Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, In Press, Online 6 May 2013"Searches of the transcriptome assembly produced by Trinity were conducted using the DeCypher Tera-BLASTP algorithm on the TimeLogic DeCypher server located at Mount Desert Biological Laboratory (Salisbury Cove, ME, USA)."
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Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest."TimeLogic Decypher Biocomputing systems (http://www.timelogic.com) were used to significantly accelerate similarity searches. Specifically, the TimeLogic Tera-BLAST algorithm was used to compare transcripts to the NCBI databases NR(non-redundant) and the viridiplantae subset of RefSeq (Pruitt et al., 2007). An expected e-value of 1e-3 and a minimum alignment length of 30 bp were used. To obtain motif-level information, accelerated Hidden Markov Model (HMM) searches were performed against local instances of Interpro HMM libraries at an e-value of 1e-10."
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Microbial Community Structure in a Seawater Flooding System in Saudi Arabia."The remaining high quality sequences were compared against the nonredundant SSU reference data set of SILVA102 using the Tera-BLAST algorithm on a TimeLogic decypher system from Active Motif, Inc., consisting of 12 boards. The Tera-BLAST results were used to screen for problematic, chimerical and eukaryotic sequences. Sequences having a best alignment covering less than 70% or having a best BLAST search hit an e-value greater than e-50 were excluded as problematic sequences."
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Peptidergic signaling in Calanus finmarchicus (Crustacea, Copepoda): In silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome."Searches of the transcriptome assembly produced by Trinity were conducted using a DeCypher Tera-BLASTP algorithm on the Mount Desert Island Biological Laboratory's (Salisbury Cove, ME, USA) TimeLogic DeCypher server."
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A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer."The raw Illumina RNA sequence data files were converted from fastq to fasta format and then aligned against the SILVA (SSURef and LSURef) database, build 106 (April 2011), using tera-blastn on Decypher Timelogic hardware-accelerated boards. The best alignment against SILVA for each RNA sequence was extracted from the tera-blastn results."
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Antennal transcriptome analysis of the chemosensory gene families in the tree killing bark beetles, Ips typographus and Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae)."The 454 reads were assembled using Seqman Ngen to generate a backbone; subsequently, the Illumina reads were mapped onto this backbone using Seqman Ngen to correct for technology-inherent read errors. The resultant contigs were annotated using a Codequest Workstation (Timelogic/Active Motif, Carlsbad, CA)."
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Pyrosequencing of the adult tarnished plant bug, Lygus lineolaris, and characterization of messages important in metabolism and development."Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against Genbank non-redundant (nr) and expressed sequence tag (est) databases (downloaded June 2008)."
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Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum)."These searches were carried out at the University of Iowa using the Tera-BLASTX implementation of the BLASTX algorithm on a TimeLogic DeCypher system (Active Motif Inc., Carlsbad, CA) using default BLASTX parameters with default e-value or maximum-hit cutoffs."
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Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen."The annotation of tree leaves was performed using TimeLogic™ TERA-BLAST of OTU representative sequences against the November 2011 release of the NCBI nt database."
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Oomycete transcriptomics database: A resource for oomycete transcriptomes."The primary annotation of the sequences was done with tera-BLASTX against a non-redundant protein database accelerated on the TimeLogic's DeCypher system."
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Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi."Functional annotation by similarity to genes from the GenBank non-redundant set using BLASTp alignments and hardware-accelerated double-affine Smith-Waterman alignments (http://www.timelogic.com) against SwissProt (http://www.expasy.org/sprot), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and eukaryotic orthologous groups of proteins (KOG)."
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In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda)."Searches of the contigs assembled from 454 pyrosequencing data were conducted using the DeCypher Tera-BLASTP algorithm on the Mount Desert Island Biological Laboratory's TimeLogic DeCypher server."
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Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum."The sequence similarity network was constructed from all-versus-all sequence matching of the proteins in version 3.2 of the Fusarium graminearum annotation (at ftp://ftpmips.gsf.de/FGDB/v32) implemented on a TimeLogic® Tera-BLAST™ (Active Motif Inc., Carlsbad, CA) system."
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The LO-BaFL method and ALS microarray expression analysis."Re-map the Agilent probes to build 36.1 of the human genome using the accelerated Tera-BLAST algorithm, as implemented on a TimeLogic-Decypher server."
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Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize."Predicted gene models were functionally annotated using [...] hardware-accelerated double-affine Smith-Waterman alignments against KEGG and KOG."
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Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici."All predicted gene models were functionally annotated by the JGI Annotation Pipeline using InterProScan (Zdobnov and Apweiler 2001) and hardware-accelerated double-affine Smith-Waterman alignments (http://www.timelogic.com/) against highly curated databases such as SwissProt (Bairoch et al. 2005), KEGG (Ogata et al. 1999), and Pfam (Bateman et al. 2004)."
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Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray"After clustering sequences, singletons and contigs were annotated again using BLASTx (Altschul et al., 1994), which was processed through a local (Mount Desert Island Biological Laboratory) TimeLogic DeCypher server (Active Motif, Inc); the ten top BLASTx hits were checked manually for consistency in annotation and degree of identity/similarity to the respective C. finmarchicus sequence."
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Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen"All predicted gene models were functionally annotated using [...] hardware-accelerated double-affine Smith–Waterman alignments (DeCypherSW; http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot/), KEGG (Kanehisa et al., 2008) and KOG (Koonin et al., 2004)."
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The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties"... and hardware-accelerated double-affine Smith–Waterman alignments (DeCypherSW; http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot/), KEGG (Kanehisa et al., 2008) and KOG (Koonin et al., 2004)."
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Characterization of the immunoglobulin repertoire of the spiny dogfish (Squalus acanthias)"To enable the design of specific primers we used individual domains from nurse shark Igs to search the spiny dogfish EST database using the Tera-BLASTP protein to DNA search function and EST dogfish multi-tissue database."
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Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis"All predicted gene models were functionally annotated using SignalP, TMHMM, InterProScan, BLASTp against NR, and hardware-accelerated double-affine Smith-Waterman alignments (DeCypherSW; http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot/), KEGG and KOG."
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Ecological structuring of bacterial and archaeal taxa in surface ocean waters"GOS metagenomes were queried by hidden Markov models (HMMs) belonging to these SCDs present in the Pfam 23.0 database (Finn, et al., 2008) using a single TimeLogic DeCypher card (Active Motif, Inc., Carlsbad, CA), and hits with E-values below 10 -10 were used for the standardization."
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Methanogenic toluene metabolism: community structure and intermediates"... using the Tera-Blast algorithm on a 16 board TimeLogic Decypher system (Active Motif, Inc.)."
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The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction"All predicted gene models were functionally annotated using SignalP (Nielsen et al., 1997), TMHMM (Melen et al., 2003), InterProScan (Zdobnov and Apweiler, 2001), BLASTp (Altschul et al., 1990) against nr, and hardware-accelerated double-affine Smith-Waterman alignments (DeCypherSW; http://www.timelogic.com/decypher_sw.html) against SwissProt (http://www.expasy.org/sprot/), KEGG (Kanehisa et al., 2008), and KOG (Koonin et al., 2004)."
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Compositions of microbial communities associated with oil and water in a mesothermic oil field"The remaining high-quality sequences were compared against the non-redundant SSURef data set of SILVA102 (Pruesse et al. 2007) using the Tera-Blast algorithm on a 16-board TimeLogic Decypher system (Active Motif, Inc.)."
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A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)"The BESs were then compared against the human reference genome NCBI build 36.1 (not including alternate assemblies), and also against db 'NT' (the nucleotide sequence collection; ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz) using the Tera-BLASTN algorithm (TimeLogic Biocomputing Solutions) with a cutoff of e-50 for the matches to the human reference genome, and only BESs with a primary hit to the human reference sequence meeting the e-50 cutoff and a next best hit with a score of e-10 or greater were included in the virtual map."
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Evaluation of microbial biofilm communities from an Alberta oil sands tailings pond"The remaining high-quality sequences were compared against the nonredundant SSU Ref data set of silva102 (Pruesse et al., 2007) using the Tera-blast algorithm on a TimeLogic Decypher system (Active Motif, Inc.) consisting of 12 boards. Tera-blast results were used to screen for problematic, chimeric, and eukaryotic sequences."
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Genome-wide metabolic network reconstruction of the picoalga Ostreococcus"A best gene match between genes in O. tauri and O. lucimarinus and genes in the union of KEGG plant genomes (meta-plant) was found using the Smith-Waterman algorithm (Smith et al., 1981) performed on a TimeLogic DeCypher (Active Motif Inc., Carlsbad, CA) gene comparison server."
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Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping"The sequenced animal was genotyped with BovineHD and BovineSNP50 BeadChips (Illumina, San Diego, California, USA). To accurately detect chromosomal positions of the SNP sites, Tera-Blast (Timelogic, USA) was used for mapping the flanking SNP sequences against both the UMD3.1 and Btau4.0 genome assemblies."
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Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris"All predicted gene models were functionally annotated using SignalP, TMHMM, InterProScan, Blastp against the nr database, and hardware-accelerated double-affine Smith-Waterman alignments (DeCypherSW; http://www.timelogic.com)"
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Effects of elevated seawater pCO2 on gene expression patterns in the gills of the green crab, Carcinus maenas"The annotation of the respective contigs included in the microarray, based on a Carcinus maneas EST library (deposited at http://www.ncbi.nlm.nih.gov), was performed by Towle et al. using BLASTX analysis on a local TimeLogic DeCypher server (Active Motif, Inc.)."
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Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline"The remaining high quality sequences were compared against the non-redundant SSU_Reference data set SILVA102 using the Tera-Blast algorithm on a 16 board TimeLogic Decypher system (Active Motif, Inc.)."
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Massive Changes in Genome Architecture Accompany the Transition to Self-Fertility in the Filamentous Fungus Neurospora tetrasperma"All predicted gene models were functionally annotated using SignalP (Nielsen et al. 1997); TMHMM (Melen et al. 2003); InterProScan (Zdobnov and Apweiler 2001); BLASTp (Altschul et al. 1990) against nr; and hardware-accelerated double-affine Smith–Waterman alignments (deCypherSW; http://www.timelogic.com/catalog/758/decyphersw) against SwissProt (Boeckmann et al. 2003), KEGG (Kanehisa et al. 2008), and KOG (Koonin et al. 2004)."
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Synganglion transcriptome and developmental global gene expression in adult females of the American dog tick, Dermacentor variabilis (Acari: Ixodidae)"... assembly of GS-FLX sequencing reads was carried out with the GS Assembler ver. 1.1.02.15 (Roche) using default parameters. Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against local custom databases consisting of the GenBank nr and EST databases (downloaded June 2008)."
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First Transcriptome of the Testis-Vas Deferens-Male Accessory Gland and Proteome of the Spermatophore from Dermacentor variabilis (Acari: Ixodidae)"Removal of primer sequence contamination and assembly of GS-FLX sequencing reads was carried out with the GS Assembler ver. 1.1.02.15 (Roche) using default parameters. Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against local custom databases consisting of the GenBank nr and EST databases (downloaded June 2008)."
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Microbial community succession in a bioreactor modeling a souring low-temperature oil reservoir subjected to nitrate injection"... using the Tera-BLAST algorithm on a TimeLogic Decypher system (Active Motif, Inc.) consisting of 12 boards."
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Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana"Prediction of microRNA candidates was performed using the miRDeep miRNA prediction program... The miRDeep code was modified [...] to utilize Decypher Timelogic hardware accelerated boards for the alignment."
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Analysis of 23S rRNA genes in metagenomes-A case study from the Global Ocean Sampling Expedition"Unaligned 23S/28S rRNA fragments retrieved by the SILVA pipeline were used to query the reference dataset of SILVA LSU release 102, using the Tera-BLASTN algorithm (Tera-BLAST™, TimeLogic Inc., Carlsbad, CA, USA)."
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Significant Alteration of Gene Expression in Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium by Plant Species"To identify P. chrysosporium homologs, the 12,438 P. placenta protein models represented on microarrays were aligned with all 10,048 v2 P. chrysosporium protein models by using Timelogic (Active Motif, Carlsbad, CA) hardware accelerated double-affinity Smith-Waterman alignments..."
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The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology"Sequence analysis: We constructed profile HMMs for the ePK, PIKK, RIO, ABC1, PDK, and alpha-kinase families with HMMer and used these to search the ORF, genomic, and EST sequences using Decypher hardware-accelerated HMMer implementation from Time Logic (Carlsbad, CA, USA)."
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Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88"All predicted gene models were functionally annotated by sequence similarity to annotated genes from the NCBI nonredundant set and other specialized databases (such as KEGG) (Kanehisa et al. 2002, 2004) using BLAST and hardware accelerated double-affine Smith-Waterman alignments (http://www.timelogic.com)."
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Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis"All predicted gene models were annotated using InterProScan and hardware-accelerated double-affine Smith-Waterman alignments (www.timelogic.com) against the SwissProt (www.expasy.org/sprot) and other specialized databases such as KEGG."
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Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets"Database searches using the BLAST were performed using the Tera-BLAST™P algorithm, open penalty 11, extend penalty 1, double-affine Smith-Waterman window 50, and maximum e-value cutoff 1 × 10-3 on TimeLogic DeCypher hardware (Active Motif, Inc., Carlsbad, CA)."
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Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1"Specialized tblastn (BLOSUM62 substitution matrix) of predicted Phage H105/1 proteins and of nine other marine phages was carried out against all six reading frames of virome nucleotide reads using DeCypher hardware (TimeLogic, Inc., Carlsbad, CA, USA)."
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Microarray-detected changes in gene expression in gills of green crabs (Carcinus maenas) upon dilution of environmental salinity"The total of 4,483 putatively unique contigs were submitted to BLASTX analysis on a local TimeLogic DeCypher server (Active Motif, Inc.) to authenticate the constituent EST results and to assist in annotating the resulting microarray."
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Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis."Sequence similarity was determined by using TimeLogic® Tera-BLAST™ (Active Motif Inc., Carlsbad, CA) for all-against-all sequence-comparison of proteins in the interaction dataset."
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Microbially Influenced Corrosion In Oil Sands Water Handling Facilities."... High quality sequences were compared against the non-redundant small subunit (SSU) ribosomal RNA database (SILVA102)11 using the Tera-BLAST (Basic Local Alignment Search Tool) algorithm on a TimeLogic Decypher system (Active Motif, Inc.)."
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Massive Parallel DNA Pyrosequencing Analysis Of The Tumor Suppressor BRG1/SMARCA4 In Lung Primary Tumors"To verify the sequencing process quality, the original 454 reads were queried (Tera-BLASTN, Decypher v7.6.2.1) against a custom database of contaminating sequences."
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Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa"For RFLP probes, homology searches used the Tera-BLAST algorithm on a TimeLogic solutions DeCypher system http://www.timelogic.com/...We also used SSR primer sequences (~20 bp in length) in pairs directly as query sequences to search for homologies against the A. thaliana pseudochromosomes, using the Tera-Probe algorithm with both gapped alignment and query filter options off."
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Carbon and sulfur cycling by microbial communities in a gypsum-treated oil sands tailings pond."... The remaining high quality sequences were compared against the nonredundant SSU ref data set of SILVA102 (24) using the Tera-BLAST algorithm on a TimeLogic Decypher system (Active Motif, Inc.) consisting of 12 boards."
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New approach for the study of mite reproduction: The first transcriptome analysis of a mite, Phytoseiulus persimilis (Acari: Phytoseiidae)"Assembled contiguous sequences, referred to as contigs, were identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic, Carlsbad, CA)."
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Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics"All predicted gene models were annotated using InterProScan and hardware-accelerated double-affine Smith-Waterman alignments (www.timelogic.com) against SwissProt (www.expasy.org/sprot) and other specialized databases like KEGG...Pfam domains were identified using TimeLogic implementation of HMMER package."
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Development and Application of Bovine and Porcine Oligonucleotide Arrays with Protein-Based Annotation."Annotation of probes on both microarrays was reassessed to take advantage of the most recent builds of the bovine and porcine genomes. To assign annotation to the 23,580 bovine oligo probes the consensus sequences were compared to the UMD2.0 build of the bovine genome with GMAP and the Decypher system GeneDetective program resulting in alignment of 21,976 consensus sequences with coverage ≥50% and identity ≥95%. Of these, 20,336 have coverage ≥95%."
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Expressed sequence tag (EST) profiling in hyper saline shocked Dunaliella salina reveals high expression of protein synthetic apparatus components."... Release 2010_06 of May 19, 2010) using Tera-BLASTP (double-banded Smith–Waterman), word size 3, gap open penalty = 11, extension penalty = 1, and a minimum significance of 1e-2 using DeCypher™ programmable logic hardware (TimeLogic, Inc., Carlsbad, CA) at ..."
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An in silico study of the genes for the isoflavonoid pathway enzymes in soybean reveals novel expressed homologues."All clustered EST consensus sequences were mapped to the genome sequences using standalone BLASTN (Altschul et al. 1990) installed on a TimeLogic CodeQuest DeCypher Engine, in order to see the results unmasked."
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Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function."... GS148-GS 149, and MOVE858 were downloaded from the CAMERA web portal and queried by all hidden Markov models (HMMs) belonging to protein domains of unknown function present in the PFAM 23.0, pfam_fs database using a single TimeLogic DeCypher card ..."
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MULTBLAST: A web application for multiple BLAST searches"TimeLogic's DeCypher system (available from Active Motif, Inc.) offers a hardware-accelerated implementation of the BLAST algorithm (TeraBLAST™). MULTBLAST utilizes these accelerated searches, thus allowing the completion of a large number of BLAST searches against large databases within a reasonable amount of time."
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A Brassica Exon Array for Whole-Transcript Gene Expression Profiling"76,687 unigenes were orientated by alignment using BLAST to Uniref100, with E-value cut-off 1E-5. Those unigenes not aligning significantly to Uniref100 were aligned to Brassica genomic scaffolds and A. thaliana genomic sequence using the TimeLogic® GeneDetective™ algorithm (Active Motif Inc., Carlsbad, CA, USA), which orientated a further 36,170 unigenes...In order to maximise the ability of the Affymetrix exon array to resolve paralogous genes which may differ at the exon level, and to detect alternative splicing, it was necessary to determine, where possible, the exon boundaries for each identified unigene or gene prediction. Since not all the unigenes had defined exon boundaries, this was achieved using the exon predictions derived from the TimeLogic® GeneDetective™ algorithm (Active Motif Inc.), where significant alignments (E-value<1E?15) existed between A. thaliana genomic sequence and B. rapa genomic scaffolds...To enrich annotation of the probes and probe-sets, A. thaliana homologues were derived from the highest scoring alignment to A. thaliana coding sequences (TAIR v9)[31] using the TimeLogic® Tera-BlastN™ algorithm (Active Motif Inc.)."
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MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing."The mirbase version 12.0 containing the mature miRNAs (http://microrna.sanger.ac.uk/ sequences) was downloaded and a blastn search with the unique sequence reads was performed using the Tera-BLASTN algorithm on a DeCypher FPGA computer."
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Neuropeptide signaling sequences identified by pyrosequencing of the American dog tick synganglion transcriptome during blood feeding and reproduction"Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against Genbank nr."
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Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae."Smith-Waterman alignments of the soybean predicted peptides corresponding to the top-ten scoring promoters was performed against the Uniprot release 14.6 (plant sequences) using a TimeLogic DeCypher system."
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Male engorgement factor: Role in stimulating engorgement to repletion in the ixodid tick, Dermacentor variabilis."Assembled contiguous sequences, herein referred to as contigs, were initially identified using the Tera-BLASTX algorithm with DeCypher (TimeLogic) against GenBank nr and ..."
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MATE Transporters Facilitate Vacuolar Uptake of Epicatechin 3'-O-Glucoside for Proanthocyanidin Biosynthesis in Medicago truncatula and Arabidopsis."The gene encoding this protein could be critical for engineering PA accumulation in forage legumes. No candidate gene was represented on the Medicago Affymetrix array previously used to study the Arabidopsis TT2-induced Medicago hairy root transcriptome (Pang et al., 2008Go). We therefore mined for Medicago MATE sequences using the Arabidopsis TT12 protein sequence to BLAST against the M. truncatula annotated genome protein database [using TimeLogic's accelerated DeCypher Tera-BLASTP algorithm]."
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Molecular Analysis of Persistent Periradicular Lesions and Root Ends Reveals a Diverse Microbial Profile."The sequences generated were compared with the GenBank database to identify the closest match using a Time Logic DeCypher TeraBlast server hosted by the Ohio Supercomputer Center (Columbus, OH)."
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Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing."mapping of all of the 3.6 million reads in this study could be mapped to either the much larger AceView database in an overnight run or to the entire human genome in 6 days using the TimeLogic DeCypher accelerator board."
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The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process."The input all-against-all BLAST matrix for the four complete proteomes is produced with the Tera-BLAST hardware implementation of BLAST with default parameter settings."
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GarlicESTdb: an online database and mining tool for garlic EST sequences."After the pre-processing step finished making EST consensus sequences, we assigned putative functions to the garlic ESTs based on BLASTN (Query Coverage ≥ 80.0%, Identity ≥ 70.0%, E-value ≤ 1.0E-20), BLASTX and TBLASTX (Match No. ≥ 50 aa, Identity ≥ 25.0%, E-value ≤ 1.0E-20) searches against the GenBank NT and NR databases (ftp://ftp.ncbi.nih.gov/blast/db/FASTA/) using a TimeLogic DeCypher system (Active Motif, Inc.)"
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Amphioxus encodes the largest known family of green fluorescent proteins, which have diversified into distinct functional classes."Searches for GFPs in other sequence sources used Blast, Psi-Blast, HMMer and Gene Detective, a hardware implementation of the Genewise algorithm (Active Motif, Carlsbad, CA)."
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BC10, a DUF266-containing and Golgi-located type II membrane protein, is required for cell-wall biosynthesis in rice (Oryza sativa L.)."Systematic identification of DUF266-containing proteins in the NCBI nr databases was performed using a TimeLogic implemented profile search engine with default parameters through a CodeQuest work station."
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Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies"An all-versus-all search of the elk dataset using four TimeLogic DeCypher boards (http://www.timelogic.com) all patterns occurring for a minimum of 20 × (based on the number of infected animals), with none of the top 100 BLAST (13) matches occurring in non-target samples, yielded 10 634 motifs specific to control and infected animals up to 5 months after infection; and 4933 motifs for animals at least 8 months after infection (motifs of 35 bases or less, using a sliding window for longer matches)."
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High-Throughput Detection of Induced Mutations and Natural Variation Using KeyPoint™ Technology"GS FLX data processing was performed using the Roche GS FLX software (Release: 1.1.03.24). Base-called reads were trimmed and filtered for quality and converted into FASTA format. A total of 666,864 and 95,222 quality filtered reads obtained from the MS and NVS libraries respectively were further processed in the KeyPoint pre-processing step. During pre-processing, the origin of the reads was identified based on the target-specific primer sequences and the six base sample identification tags.This step was implemented in a custom Perl script that used the Semi Global Smith Waterman algorithm within a TimeLogic DeCypher system (Active Motif, Inc.)."
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A robust linkage map of the porcine autosomes based on gene-associated SNPs"Annotation of the SNP-containing genes. Sequences surrounding the SNPs were subjected to blast analysis on a DeCypher FPGA computer using the accelerated BLASTNH algorithm (Timelogic/Active Motif)."
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A Snapshot of CNVs in the Pig Genome"Subsequently, we used Tera-Probe™ an algorithm similar to the BLAST sequence search algorithm but optimized for small oligonucleotide sequences. Tera-Probe™ was used to query the probes within the CNVRs against the newest available version of the Sus Scrofa assembly...""The Tera-BLAST™N sequence similarity algorithm was used to query the CNVR sequences against the pig Unigene and the Refseq vertebrate mammalian mRNA databases."
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Graph-based sequence annotation using a data integration approach"...the “TimeLogic” (http://www.timelogic.com) implementation of HMMER was used because it has a higher throughput and sensitivity compared to the BLAST approach."
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Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns"5,484 ESTs (Expressed Sequence Tags) and 4,242 gDNAs of N. ovalis were sequenced. Vectors and linkers were automatically filtered out of sequences. First the vector pieces were detected using a BlastN search against their respective vector sequences on a TimeLogic DeCypher...""...All sequence comparisons were run on a DeCypher TimeLogic using the Smith-Waterman algorithm for pairwise sequence comparisons and Hidden Markov Models for sequence-to-profile comparisons, active motifs included. The output was subsequently analyzed in a Linux environment using Perl scripts."
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Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies"...An all-versus-all search of the elk dataset using four TimeLogic DeCypher boards (http://www.timelogic.com) all patterns occurring for a minimum of 20 x (based on the number of infected animals), with none of the top 100 BLAST (13) matches occurring in non-target samples, yielded 10 634 motifs specific to control and infected animals up to 5 months after infection; and 4933 motifs for animals at least 8 months after infection (motifs of 35 bases or less, using a sliding window for longer matches)..."
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Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression"...The resulting sequences were then compared against the GenBank non-redundant database using the BLASTX algorithm. Batch blasts were performed using the CodeQuest system..."
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The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan"...TIGR, and in-house HMM ( SI Text, Figs. S3 and S4 ) with Global and Glocal models were performed with a hardware-accelerated DeCypher system (Active Motif). E value cutoffs of e = 10 were used to pick up repeated elements whose individual scores were very low..."
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Osteogenic gene regulation and relative acceleration of healing by adenoviral-mediated transfer of human BMP-2 or -6 in equine osteotomy and ostectomy models"The names and functions of genes were annotated by the commercially available software (BlastN, TimeLogic Corp, Carlsbad, CA"
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Development and Use of an Efficient System for Random mariner Transposon Mutagenesis To Identify Novel Genetic Determinants of Biofilm Formation in the Core Enterococcus faecalis Genome"To identify segments of the E. faecalis V583 genome that are absent from the genome of strain OG1RF, the partially assembled OG1RF contigs were obtained from the Baylor College of Medicine website. The nucleotide sequences of all annotated V583 open reading frames (ORFs) (obtained from TIGR) were compared with the OG1RF contigs using the Smith-Waterman algorithm computed with the TimeLogic DeCypher software program (Active Motif, Inc.). The top-ranked hit for each V583 ORF was examined for percent alignment with the OG1RF contig. Hits with greater than 90% alignment were considered matches and scored as present in the OG1RF genome. Tabulation of the results on an ORF-by-ORF basis revealed the presence of multigene gaps missing from the OG1RF genome, some of which were previously known."
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A Nearest Neighbor Approach for Automated Transporter Prediction and Categorization from Protein Sequences"...order to demonstrate the proposed approach, a prediction web server, as well as a command line interface, was implemented. The Decypher hardware system, provided by Active Motif Incorporation, was utilized to conduct the BLAST search and multiple CPU/computers..."
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Genome-Based Analysis of Chlamydomonas reinhardtii Exoribonucleases and Poly(A) Polymerases Predicts Unexpected Organellar and Exosomal Features Abstract"...implemented at the Boyce Thompson Institute. Arabidopsis (version...domain database (Bateman et al. 2004) with a TimeLogic Decypher system ( http://codequest.bti.cornell.edu/chlre ). The same sequences..."
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The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution"...We also used tBLASTx to search against the Human (Hs) Unigene database (Build 201), the NCBI Chicken protein database (downloaded May 17, 2007) and the Chicken International Protein Index (IPI, Release 3.26). Default parameters were used for all BLASTs, which were performed locally with TimeLogic Server..."
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Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)"...word size 3, gap open penalty=11, extension penalty=1, and a minimum significance of 1e5 using DeCypher programmable logic hardware (TimeLogic, Inc., Carlsbad, CA, USA) at the Nevada Center for Bioinformatics. Functional categories were assigned..."
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A nearest neighbor approach for automated transporter prediction and categorization from protein sequences"In order to demonstrate the proposed approach, a prediction web server, as well as a command line interface, was implemented. The DeCypher hardware system, provided by Active Motif Incorporation, was utilized to conduct the BLAST search and multiple CPU/computers were run in parallel to perform HMM modeling and scoring."
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Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution"The protein sequences of the microsporidium Encephalitozoon cuniculi and of 25 fungi ... were downloaded rom the corresponding sequencing projects. Similarity scores between the proteomes were computed using the Smith–Waterman P algorithm (Smith & Waterman 1981) on a TimeLogic DeCypher (matrix: Blosum62; e-value cut-off: 0.01; low-complexity filter on). The orthologous groups were constructed by an approach similar to that used for the COGs (Tatusov et al. 2000)."
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Selecting Folded Proteins from a Library of Secondary Structural Elements"All secondary structural elements in the shuffling pool were selected from unique E. coli proteins with structures on file in the Protein Data Bank (PDB). PDB files of these proteins were submitted to the program PROMOTIF and the output files annotating the elements of secondary structure and the primary sequence of each element, as well as loop primary sequence data from the Sloop database, were submitted to DeCypher FrameSearch BLAST (Active Motif, Inc.) to obtain the E. coli nucleotide sequences encoding each element."
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Computational prediction and experimental validation of Ciona intestinalis microRNA genes"...The final step in the mRNA target prediction process examined the mRNA targets for conservation in C. savignyi. Currently, predicted transcripts of C. savignyi do not exist. C.savignyi "pseudo" mRNAs were generated as follows. The tera-tblastn program on the TimeLogic board aligned the C.intestinalis mRNA gene sequences against the entire C. savignyi genome. The top match of the C. savignyi genome to each of the mRNA sequences was classified as an orthologous C. savignyi mRNA. The target prediction code was applied to the C. savignyi subsequences, to check that miRNAs matched the 3'UTR of orthologous genes to C. intestinalis, according to the seed match criteria described earlier..."
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Microarray Expression Profiles of 20.000 Genes across 23 Healthy Porcine Tissues"...EST clusters for human gene transcripts in NCBI's RefSeq database release 17 [28] were created using BLASTN sequence similarity program implemented to run on a DeCypher computer [http://www.timelogic.com] with P-value at or below 10−8..."
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Development of a physical map of the soybean pathogen Fusarium virguliforme based on synteny with Fusarium graminearum genomic DNA"...The identification of exonic fragments was carried out using TimeLogic® GeneDetective™ (Active Motif Inc., Carlsbad, CA) In order to directly relate the exons to the associated BES fragments and to accommodate the processing restrictions of Gene Detective, the identical 36 Mbp single sequence used for sequence comparison was divided into smaller, 999 bp linear order fragments, then tested these against the non-redundant fungal EST database (downloaded from NCBI on Nov 16, 2006; 886,100 fungal ESTs). We used only the top two ranked hits for each sequence and removed overlapping results..."
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Patent Application: Novel kinases"...The PFAM alignments were downloaded from http://pfam.wustl.edu/hmmsearch.shtml and the HMMr searches were run locally on a Timelogic computer...""...Novel kinases were identified from the Celera human genomic sequence databases, and from the public Human Genome Sequencing project (http://www.ncbi.nlm.nih.gov/) using a hidden Markov model (HMMR) built with 70 mammalian and yeast kinase catalytic domain sequences. These sequences were chosen from a comprehensive collection of kinases such that no two sequences had more than 50% sequence identity. The genomic database entries were translated in six open reading frames and searched against the model using a Timelogic Decypher box with a Field programmable array (FPGA) accelerated version of HMMR2.1..."
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EDR2 negatively regulates salicylic acid-based defenses and cell death during powdery mildew infections of Arabidopsis thaliana"...Domains present in EDR2 were identified with the Hidden Markov Model program... [59. Stanford TimeLogic Hidden Markov Model Software]..."
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Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis"...We first performed all-against-all double affine Smith-Waterman alignments of the peptides in X. laevis and X. tropicalis using a TimeLogic DeCypher system (Active Motif, Inc., 1914 Palomar Oaks Way, Suite 150, Carlsbad, CA. 92008) with BLOSUM62 scoring matrix, gap opening penalty -15, gap extension penalty -2 until gap size 10, with no additional extension penalties. We identified the conserved four-fold degenerate amino acids within the alignments, extracted the corresponding codons in the underlying DNA sequence and calculated the 4 DTv distances (D4DTv) between each aligning pair as the fraction of four-fold degenerate (4D) third codon positions in which transversions are observed to have occurred. This provides a measure of the evolutionary distances between genes that is largely independent of the gene families, unlike measures based on peptides...""...The zebrafish doublets shown in Figure 1a were determined as follows: the Ensembl [39] models v. 24.4.1 were aligned to each other and to the Ensembl models v. 26.35.1 for human on Timelogic Decypher™ using the same parameter settings as for the frog aligments, and 4 DTv distances were determined for each pair with 25 or more 4D codon sites..."
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Patent Application: Novel essential fungal polynucleotides, polypeptides, and methods of use"Global sequence similarity searches were performed using the amino acid sequences of all the conserved essential polynucleotide sequence against a non-redundant protein database using the Smith-Waterman algorithm with default parameters on a TimeLogic DeCypher system..."
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SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation"...sensitivity. EST clustering was performed using the accelerated BLAST (Altschul et al., 1997) based TeraClu algorithm on a DeCypher FPGA Computer (Timelogic/Acitve Motif) followed by cluster assembly using Phrap (Green,P., unpublished data). EST and contig.."
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The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation"...Predicted genes were annotated by using double-affine Smith-Waterman (TimeLogic) alignments against proteins from the National Center for Biotechnology In-formation nonredundant protein database, protein..."
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Genome-Wide Identification and Comparative Analysis of Coiled-Coil Proteins"First, coiled-coil sequences were masked by replacing amino acids predicted to be inside a coiled-coil region with the generic letter X. The masked sequence set was then compared in an all-against-all approach using the Smith-Waterman (SW Search) sequence comparison algorithm [20]. Smith-Waterman analysis was accomplished with the TimeLogic De-Cypher system using the blossum62 scoring matrix."
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Structural and Functional Diversity of the Microbial Kinome"...Discovery and classification of kinase genes. Sequences used consisted of 17,422,766 open reading frames from GOS, 3,049,695 predicted open reading frames from prokaryotic genomes, and 2,317,995 protein sequences from NCBI-nr of February 10, 2005, as described [22]. Profile HMM searches were performed with a Time Logic Decypher system (Active Motif) using in-house profiles for ePK, Haspin, Bub1, Bud32, Rio, ABC1 (UbiB), PI3K, and AlphaK domains, as well as Pfam profiles [43] for ChoK, APH, KdoK, and FruK, and TIGRFAM profiles [44] for HSK2 (thrB_alt), UbiB, and MTRK. A number (69) of additional ePK-annotated models from Superfamily 1.67 [45] were used to capture initial hits but not for further classification. Initial hits were clustered and re-run against all models, and each model was rebuilt and rerun three to seven times using ClustalW [46], MUSCLE [47], and hmmalign (http://hmmer.janelia.org) to align, followed by manual adjustment of alignments using Clustal and Pfaat [48] and model building with hmmbuild. Low-scoring members of each family (e > 1 × 10−5) were used as seeds to build new putative families, and profile–profile and sequence–profile alignments were used to merge families into a minimal set (Dataset S2). A motif-based Markov chain Monte Carlo multiple alignment model [49] based on the conserved motifs of Figure 3 was run independently and used to verify HMM hits and seed new potential families for blast-based clustering, model building, and examination for conserved residues. Final family assignment was by scoring against the set of HMM models, with manual examination of sequences with borderline scores (e > 1 × 10−5 or difference in e-values between best two models >.01)..."
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The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families"...Searching sequences using profile HMMs. The full set of 7,868 Pfam release 17 models was used, along with additional nonredundant profiles from TIGRFAM (1,720 of 2,443 profiles; version 4.1). HMM profiling was carried out using a TimeLogic DeCypher system (Active Motif, Inc.) and took 327 hours in total (on an eight-card machine). A sequence was considered as matching a Pfam (fragment model) if its sequence score was above the TC score for that Pfam and had an E-value ≤ 1 × 10−3. It was considered as matching a TIGRFAM if the match had an E-value ≤ 1 × 10−7..."
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PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results"...PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software..."
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DarkHorse: a method for genome-wide prediction of horizontal gene transfer"...BLAST searches were performed using either the DeCypher Tera-BLAST™ (Active Motif, Inc. Carlsbad, California, USA) or NCBI BLAST program..."
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Evolution of protein complexes by duplication of homomeric interactions"...We used the Smith-Waterman implementation of the TimeLogic's DeCypher® accelerated hardware..."
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Gene discovery in Carcinus maenas and Homarus americanus via expressed sequence tags"All of the resulting contigs and singlets were submitted to blastx analysis using the Tera-BlastP algorithm (translated nucleotide sequence versus protein sequence) on a DeCypher server (TimeLogic), with reference to the non-redundant protein sequence database from NCBI. Positive hits with an E-value <0.0001 were obtained for 44.7% of the Carcinus contigs and 33.9% of the Homarus contigs, and for 47.4% of the Carcinus singlets and 39.3% of the Homarus singlets"
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The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment"Sequence similarity was detected by the Smith and Waterman method (Smith Waterman, 1981) on a DeCypher hardware-accelerated system (Active Motif, Carlsbad, CA)."
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Changes in Periodontal Health Status Are Associated with Bacterial Community Shifts as Assessed by Quantitative 16S Cloning and Sequencing"...amplicon. The sequences generated were compared to the GenBank database to identify the closest match using a Time Logic DeCypher TeraBlast server hosted by the Ohio Supercomputer Center. Sequences with low homology to GenBank entries were screened for chimeras..."
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What Makes Species Unique? The Contribution of Proteins with Obscure Features"...BLAST comparisons of PDFs and POFs among different proteomes were performed using TeraBLAST running on an accelerated DeCypher server....'All-against-all' comparisons used to generate sets of species-specific proteins for both PDFs and POFs from Sc, Sp, At, Os, Dm, Ag, Ce, Mm, Rn and Hs were performed using TeraBLAST running on an accelerated DeCypher server [32], with a cutoff threshold of 10-6."
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Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis"...a DeCypher hardware-accelerated system (Active Motif) was used to perform HMMER searches against nucleic acid sequences."
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A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation"We searched the genomes for homologs using the Smith-WatermanP algorithm [22] on a TimeLogic DeCypher in all query-database combinations (matrix: Blosum62; e-value cutoff:100). In the case of spurious asymmetries in the similarity search (e.g. two sequences giving different alignments depending on which was the query), the results are the average of two values, including both reciprocal experiments..."
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Zfp312 is required for subcortical axonal projections and dendritic morphology of deep-layer pyramidal neurons of the cerebral cortex"...species is summarized in the dendrogram. Amino acids alignments were performed by using the ClustalW algorithm available from DeCypher (http://coe02.ucalgary.ca), and minor corrections were made manually."
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Coiled-coil protein composition of 22 proteomes – differences and common themes in subcellular infrastructure and traffic control"Smith-Waterman comparison was conducted using the TimeLogic Smith-Waterman implementation at OSC and the Blosum62 scoring matrix on all unique sequences in the combined sequences set. Sequences with masked coiled-coil domains were used as query on unmasked sequence sets as target. A P-score cut-off of 1.0e-03 was used as a threshold for selecting sequence similarity relationships. For sequences to be characterized as pair-wise similar and recovered for use in the clustering analysis, the P-score value must be less than this threshold based on the query-target Smith-Waterman comparison..."
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Resolving tylenchid evolutionary relationships through multiple gene analysis derived from EST data"Gene-for-gene, pairwise comparisons were made between different species using the Hardware Accelerated, Tera-BLAST algorithm (Time-Logic, Crystal Bay, NV) executed on three TimeLogic DeCypher nodes."
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Identification of Candidate Periodontal Pathogens and Beneficial Species by Quantitative 16S Clonal Analysis"The sequences generated were compared to the GenBank database to identify the closest relatives by using a Time Logic DeCypher Tera BLAST server hosted by the Ohio Supercomputer Center."
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Zfp312 is required for subcortical axonal projections and dendritic morphology of deep-layer pyramidal neurons of the cerebral cortex"Amino acids alignments were performed by using the ClustalW algorithm available from DeCypher..."
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Structural and functional characterization of CFE88: Evidence that a conserved and essential bacterial protein is a methyltransferase"A DeCypher hardware-accelerated bioinformatics system (TimeLogic, Inc.) was used to perform the Smith-Waterman, FrameSearch, and HMMER searches described below. The Smith-Waterman algorithm (Smith and Waterman 1981) was used to compare the amino acid sequence of CFE88 with protein sequences from completed microbial genomes, and the FrameSearch algorithm (Edelman et al. 1995) was used to compare CFE88 with nucleotide sequences from unfinished microbial genomes, using the DeCypher system as described in Healy (2003)."
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Databases and Information Integration for the Medicago truncatula Genome and Transcriptome"... for CCGB bioinformatics since targets are created for different platforms (Linux clusters, single machine use, TimeLogic DeCypher server) and these different targets must remain coherent and consistent. ..."
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Structural and functional characterization of CFE88: evidence that a conserved and essential bacterial protein is a methyltransferase"Bioinformatics analysis and threading: A DeCypher hardware-accelerated bioinformatics system (TimeLogic, Inc.) was used to perform the Smith-Waterman, FrameSearch, and HMMER searches..."
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An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing"Matches were detected with either the BLASTZ computer program or a hardware-optimized Smith-Waterman algorithm (TimeLogic, Carlsbad, CA)....Smith-Waterman alignments were generated by using a DeCypher machine (TimeLogic, Carlsbad, CA)."
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A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase"The human ASM protein sequence, corresponding to the predicted phosphoesterase domain (amino acid residues 201–472), was used to search for homologs. Three common search algorithms, BLAST, Smith-Waterman, and FASTA (Smith and Waterman 1981; Altschul et al. 1990; Pearson 1990), were used to search for possible templates in three protein databases—GenPept (database dated October 2000) (Benson et al. 2000), SwissProt (August 1999 version) (Bairoch and Boeckmann 1994), and Protein Data Bank (PDB; August 1999 version) (Berman et al. 2000)...With the exception of FASTA, all database searches were run using TimeLogic DeCypher."
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Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays"Abstract: We have developed a software package called Osprey for the calculation of optimal oligonucleotides for DNA sequencing and the creation of microarrays based on either PCR-products or directly spotted oligomers. It incorporates a novel use of position-specific scoring matrices, for the sensitive and specific identification of secondary binding sites anywhere in the target sequence. Using accelerated hardware is faster and more efficient than the traditional pairwise alignments used in most oligo-design software. Osprey consists of a module for target site selection based on user input, novel utilities for dealing with problematic sequences such as repeats, and a common code base for the identification of optimal oligonucleotides from the target list. Overall, these improvements provide a program that, without major increases in run time, reflects current DNA thermodynamics models, improves specificity and reduces the user's data preprocessing and parameterization requirements. Using a TimeLogic™ hardware accelerator, we report up to 50-fold reduction in search time versus a linear search strategy. Target sites may be derived from computer analysis of DNA sequence assemblies in the case of sequencing efforts, or genome or EST analysis in the case of microarray development in both prokaryotes and eukaryotes."
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Computational Identification and Characterization of Novel Genes from Legume"In the final BLAST iteration, the remaining legume-specific TCs were then compared to EST_others using the DeCypher Bioinformatics Accelerator running the Tera-BLAST hardware accelerated version of BLAST (TimeLogic, Crystal Bay, NV), which was housed in the Center for Computational Genomics and Bioinformatics at the University of Minnesota."
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Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA target"...iRNA target gene prediction was performed by aligning miRNA sequences with target mRNA sequences using the TimeLogic implementation of the Smith-Waterman nucleotide-alignment algorithm..."
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Sequence and Organization of the Neodiprion lecontei Nucleopolyhedrovirus Genome"If difficulties were encountered identifying homologues with standard protein-protein BLAST (blastp) searches, further analysis was done using [...] Smith Waterman similarity searches using DeCypher with default settings."
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S100 Proteins in the Epidermis"The ClustalW sequence comparison program, decypher.stanford.edu, was used to align the protein sequences."
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Identification of Cathepsin B as a Mediator of Neuronal Death Induced by Ab-activated Microglial Cells Using a Functional Genomics Approach"...a comprehensive homology analysis was conducted using a Blast algorithm against the RefSeq (NCBI) data base on accelerated hardware (TimeLogic)."
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The SUPERFAMILY database in 2004: additions and improvements"Genome assignments: Using TimeLogic DeCypher hardware, the library has been used to carry out assignments to predicted proteins from all completely sequenced genomes, the Swiss-Prot and TrEMBL databases and other sequence collections."
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Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes"...The predicted proteins were submitted to Hidden Markov Model searches, implemented in timelogic (TimeLogic, Carlsbad, CA), to determine their multidomain PKS protein structures... ... The predicted proteins were submitted to Hidden Markov Model searches, implemented in TimeLogic (TimeLogic, Carlsbad, CA), to determine their multidomain structures..."
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Finding Homologs to Nucleic Acid or Protein Sequences Using the Framesearch Program"Illustration of how insertion and deletion errors affect alignments generated by the six-frame-translated Smith-Waterman algorithm. Note that this example was generated on a DeCypher genomics accelerator, manufactured by TimeLogic.""...on a TimeLogic DeCypher system one can specify a cutoff quality score or statistical probability score as well as the maximum numbers of scores and alignments to present""...the Timelogic implementation of Framesearch found on their DeCypher systems has a much more flexible provision for specifying which strand to search"
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Whole-Genome Analysis of Two-Component Signal Transduction Genes in Fungal Pathogens"... Conserved Pfam domains were identified by using the DeCypher hidden Markov model (protein sequence versus hidden Markov model) search algorithm ..."
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Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach"...Meloidogyne sequences from NCBI were analyzed using the Tera-BLAST Hardware Accelerated BLAST algorithm (TimeLogic...). Single FASTA files were submitted for three six-phase translated Tera-TBLASTX queries against six-phase translated C. elegans and Drosophila genomic databases..."
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A comparative analysis of HGSC and Celera human genome assemblies and gene sets"The PFAM 7.0 database release, containing 3360 HMMs, was used to analyze gene sets for their protein domain content. For this analysis, the HMMER software package (Eddy, 1998) or its compatible implementations from Paracel and TimeLogic (http://www.timelogic.com) were run on a Linux computing cluster (150 CPUs, Linux Networks), a Paracel GENEMATCHER machine, and a TimeLogic Decypher machine, respectively."
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MGView: an alignment and visualization tool to enhance gap closure of microbial genomes"...The TimeLogic system is currently implemented with MGView to accelerate the alignment operation ( www.timelogic.com ).... ... Together with the backbone genome nucleotide file, the TimeLogic BLAST report is used to produce two major PDF output files, MGMap and MGTrack ..."
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A role for receptor tyrosine phosphatasezeta in glioma cell migration"Gene identification of clones was performed by a rapid and comprehensive homology analysis of the sequenced ESTs using Blast and Smith–Waterman algorithms with NCBI, Unigene, Swiss-Prot/TrEMBL (GeneBio, Geneva, SW, USA), and Derwent patent (Alexandria, VA, USA) databases, and accelerated hardware (TimeLogic)."
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ELL-associated factor 2 (EAF2), a functional homolog of EAF1 with alternative ELL binding properties"...were conducted with the basic local alignment search tool (BLAST) search algorithm and with the DeCypher II Similarity Search System. ... ... acid similarity previously observed between EAF1 and AF4 family members, we used the BLASTP and DeCypher II Smith Waterman algorithms to identify a comparable region of EAF2 with limited similarity to ..."
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The Protein Kinase Complement of the Human Genome"Use of HMM to discover ePK domains: Local and global HMM models were built with the HMMer package (http://hmmer.wustl.edu) and were searched against sequence databases using the Decypher hardware-accelerated HMMer implementation from TimeLogic."
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The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs"... sanger.ac.uk/Software/Pfam/; Bateman et al. , 2002) using the HMMER2 software (http://hmmer.wustl.edu/) on a hardware accelerated Decypher box to build up a mapping of HOMSTRAD and Pfam families...."
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Using Genomic Resources to Guide Research Directions. The Arabinogalactan Protein Gene Family as a Test Case"... position-specific score matrix (HMM) was then used to search the Arabidopsis protein database at the DeCypher Web site ( http://decypher2.stanford.edu/algo-hmm/ HMM_ha.html-ssi). ... ... that was generated by HMMbuild was used to search the Arabidopsis protein database from the DeCypher Web site [at Stanford] by pasting the model into the appropriate box..."
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Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction"... NM_001014) and S. cerevisiae S10 (Accession : NP_014936) are aligned with the ClustalW program (http://decypher.stanford.edu) and schematically presented with the Boxshade program + Identical residues are boxed in black ..."
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A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)"Timelogic's Decypher FrameSearch algorithm was used to detect and guide the correction of frameshifts caused by indels."
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The EBI SRS server—recent developments"...pattern matching; (4) HMMPfam from the HMMER package (http: //hmmer.wustl.edu/) or HMMS implemented on a Decypher machine from TimeLogic that scans sequences against the Pfam collection of protein domain HMMs (hidden ..."
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Recurrence quantification analysis reveals interaction partners in paramyxoviridae envelope glycoproteins"...the matrices of between-sequence distances are derived by the multiple alignments algorithm ClustalW, developed by Thompson et al. using the DeCypher server of TimeLogic Corporation."
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VmrA, a Member of a Novel Class of Na+-Coupled Multidrug Efflux Pumps from Vibrio parahaemolyticus"... The dendrogram was obtained by using CLUSTAL W and Decypher of Stanford University computer system..."
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InterProScan – an integration platform for the signature-recognition methods in InterPro"[Pfam and SMART domains identified using TimeLogic™ HMM Search.]"
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Molecular Modeling of the Extracellular Domain of the RET Receptor Tyrosine Kinase Reveals Multiple Cadherin-like Domains and a Calcium-binding Site"Multiple sequence alignments were obtained by CLUSTALW running at the Decypher hardware accelerator (www.timelogic.com)."
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Trace amines: Identification of a family of mammalian G protein-coupled receptors"Amino acid sequences for each receptor spanning from the start of TMI to the end of TMVII were aligned by using the CLUSTALW algorithm and the tree constructed by the NJ method on a DecypherII Bioaccelerator (TimeLogic, Reno, NV)."
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EAF1, a novel ELL-associated factor that is delocalized by expression of the MLL-ELL fusion protein"Database searches were conducted with the BLAST search algorithm and with the DeCypher II Similarity Search System."
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Complete DNA Sequence and Analysis of the Large Virulence Plasmid of Shigella flexneri"Each ORF was initially searched against the GenPept protein database using the DeCypher II system, to determine identity or match with known proteins. After subsequent inspection and further analysis of many of the ORFs, annotations were created."
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Glycoprotein E of Varicella-Zoster Virus Enhances Cell-Cell Contact in Polarized Epithelial Cells"Sequences were compared by CLUSTALW multiple-sequence alignment using the DeCypher bioinformatics supercomputer (Center for Molecular and Genetic Medicine, Stanford University)."
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The Genome Sequence DataBase"Frame Search can be used to search a protein query sequence against a dynamically translated nucleotide database. As a consequence of the Smith–Waterman basis of this algorithm and the dynamic translation of the query sequence or target database, Frame Search is a computationally intensive algorithm. However, based upon internal testing and benchmarking of Frame Search on the Decypher system, we have found that it is comparable in speed to tblastx searches."
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A Genome-Wide Search for Synaptic Vesicle Cycle Proteins in Drosophila"Genes were considered homologs if the blast score was less than e?15 and aligned over >30% of the vertebrate protein sequence. In some cases, two genomic sequences for a single gene were identified due to a gap in the genomic sequence, in which case the blast scores for both genomic sequences are listed. When known Drosophila genes were previously identified, the Drosophila name is in bold, and the percent identity/similarity was determined using the Smith-Waterman algorithm (http://www.timelogic.com/)."
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The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer"Searches of the protein databases for amino acid similarities were performed using the DeCypher II system (TimeLogic Inc.) to assign known functions or suggest functions for new ORFs."
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The Phytophthora Genome Initiative Database: informatics and analysis for distributed pathogenomic research"...and it will soon be possible to apply to these sequences the more advanced similarity search algorithms available on NCGR’s TimeLogic server..."
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The Genome Sequence DataBase: towards an integrated functional genomics resource"A TimeLogic DeCypher II was recently acquired to provide a server for homology searching using several algorithms... The DeCypher includes accelerated versions of Smith-Waterman, Frame Search, Symmetric Frame Independent and Profile Search that will become publicly available for searching data from GSDB during the first half of 1999."
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Characterization of Varicella-Zoster Virus Glycoprotein K (Open Reading Frame 5) and Its Role in Virus Growth"Alignment of gK proteins from alphaherpesviruses with the DeCypher II Smith-Waterman Example program (Center for Molecular and Genetic Medicine, Stanford University) shows substantial similarity to VZV. aa, amino acid(s)."
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Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure"Smith-Waterman comparisons were conducted on a TimeLogic DeCypher II machine using the affine Smith-Waterman application."
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Complete DNA Sequence and Detailed Analysis of the Yersinia pestis KIM5 Plasmid Encoding Murine Toxin and Capsular Antigen"For the first pass, amino acid sequences were searched against the current GenPept database by using the BLOSUM62 matrix by the DeCypher II System (TimeLogic, Inc., Incline Village, Nev.)."
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DNA Sequencing and Analysis of the Low-Ca2+-Response Plasmid pCD1 of Yersinia pestis KIM5."ORF amino acid sequences were searched against SWISS-PROT 34 by using the BLOSUM26 matrix, with the DeCypher II System (TimeLogic Inc.)."
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Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning"Sequences were assembled and analyzed for redundant clones using the DeCypher II PC board and accompanying software (Time Logic)."
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The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7"ORF amino acid sequences were searched against SWISS-PROT 34 and GenPept 104 using the BLOSUM62 matrix and the Smith-Waterman algorithm accelerated by the DeCypher II system (TimeLogic Inc.) to assign known functions or suggest functions for new ORFs."
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Molecular Evolution of a Pathogenicity Island from Enterohemorrhagic Escherichia coli O157:H7dagger"Each ORF was annotated based on protein sequence searches (DeCypherII hardware/software system; TimeLogic, Inc.) against a combined SwissProt release 34 and trEMBLSP release 1 database."
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The Complete Genome Sequence of Escherichia coli K-12"The function of new translated sequences was imputed from sequence similarity... Similarity searches were conducted using both the DeCypher II hardware-software system (Time Logic Inc., Incline Village, NV) and the PepPepSearch program of the Darwin suite at Zurich..."
