| Papers
and Patents Citing Use of 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). Examples
for referencing TimeLogic products are found below. We greatly appreciate
hearing about new citations for our products. Please let
us know about your upcoming publications that cite our products!
- The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution
Kirstin L Replogle , Arthur P Arnold , Gregory F Ball , Mark Band , Staffan Bensch , Eliot A Brenowitz , Shu Dong , Jenny Drnevich , Margaret Ferris , Julia M George , George Gong , Dennis Hasselquist , Alvaro G Hernandez , Ryan Kim , Harris A Lewin , Lei Liu , Peter V Lovell , Claudio V Mello , Sara Naurin , Sandra Rodriguez-Zas , Jyothi Thimmapuram , Juli Wade and David F Clayton
BMC Genomics 2008 |
Published: 18 March 2008
...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...
- Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM)
John C. Cushman, Richard L. Tillett, Joshua A. Wood, Joshua M. Branco, and Karen A. Schlauch
J. Exp. Bot., Mar 2008; 10.1093/jxb/ern008
...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...
- Computational prediction and experimental validation of Ciona intestinalis microRNA genes
Norden-Krichmar TM, Holtz J, Pasquinelli AE, Gaasterland T
BMC Genomics 2007, 8:445 (29 November 2007)
...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...
- Microarray Expression Profiles of 20.000 Genes across 23 Healthy Porcine Tissues
Henrik Hornshøj, Lene Nagstrup Conley, Jakob Hedegaard, Peter Sørensen, Frank Panitz, Christian Bendixen
PLoS ONE 2(11): e1203 (Published 21 Nov 2007)
...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...
- Development of a physical map of the soybean pathogen Fusarium virguliforme based on synteny with Fusarium graminearum genomic DNA. Shultz JL, Ali S, Ballard L, Lightfoot DA
BMC Genomics 2007, 8:262 (3 August 2007)
...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...
- Patent Application: Novel kinases.
Whyte; David; (Belmont, CA) ; Manning; Gerard; (Menlo Park, CA) ; Caenepeel; Sean; (Walnut Creek, CA), Sugen Corporation
US PTO record 20070202107 (August 2007)
...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...
- EDR2 negatively regulates salicylic acid-based defenses and cell death during powdery mildew infections of Arabidopsis thaliana
Vorwerk S, Schiff C, Santamaria M, Koh S, Nishimura M, Vogel J, Somerville C, Somerville S
BMC Plant Biology 2007, 7:35 (6 July 2007)
...Domains present in EDR2 were identified with the Hidden Markov Model program... [59. Stanford TimeLogic Hidden Markov Model Software]...
- Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis
Hellsten U, Khokha MK, Grammer TC, Harland RM, Richardson P, Rokhsar DS
BMC Biology 2007, 5:31 (25 July 2007)
...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...
- Patent Application: Novel essential fungal polynucleotides, polypeptides, and methods of use.
Louis K. Wille, Bristol-Myers Squibb Company
US PTO record 20070172881 (July 2007)
...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...
- SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Frank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B. Madsen, Anette Høj, Rikke K. Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob H. Havgaard, Søren Brunak, Merete Fredholm, and Christian Bendixen
Bioinformatics, Jul 2007; 23: i387 - i391.
...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..
- The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation
Brian Palenik, Jane Grimwood, Andrea Aerts, Pierre Rouzé, Asaf Salamov, Nicholas Putnam, Chris Dupont, Richard Jorgensen, Evelyne Derelle, Stephane Rombauts, Kemin Zhou, Robert Otillar, Sabeeha S. Merchant, Sheila Podell, Terry Gaasterland, Carolyn Napoli, Karla Gendler, Andrea Manuell, Vera Tai, Olivier Vallon, Gwenael Piganeau, Séverine Jancek, Marc Heijde, Kamel Jabbari, Chris Bowler, Martin Lohr, Steven Robbens, Gregory Werner, Inna Dubchak, Gregory J. Pazour, Qinghu Ren, Ian Paulsen, Chuck Delwiche, Jeremy Schmutz, Daniel Rokhsar, Yves Van de Peer, Hervé Moreau, and Igor V. Grigoriev
PNAS, Apr 2007; 10.1073/pnas.0611046104
...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...
- The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families.
Shibu Yooseph*, Granger Sutton, Douglas B. Rusch, Aaron L. Halpern, Shannon J. Williamson, Karin Remington, Jonathan A. Eisen, Karla B. Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S. Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachimiak, Christopher van Belle, John-Marc Chandonia, David A. Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benjamin J. Raphael, Vineet Bafna, Robert Friedman, Steven E. Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Susan S. Taylor, Robert L. Strausberg, Marvin Frazier, J. Craig Venter
PLoS Biology Vol. 5, No. 3, e16 doi:10.1371/journal.pbio.0050016
...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...
- Structural and Functional Diversity of the Microbial Kinome
Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G
PLoS Biology Vol. 5, No. 3, e17 doi:10.1371/journal.pbio.0050017
...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)...
- PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results.
He J, Dai X, Zhao X
BMC Bioinformatics 2007, 8:53 (9 February 2007)
...PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software...
- DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Sheila Podell and Terry Gaasterland.
Scripps Genome Center, Scripps Institution of Oceanography, University of California at San Diego, Gilman Drive, La Jolla, CA 92093-0202, USA
Genome Biology 2007, 8:R16.
...BLAST searches were performed using either the DeCypher Tera-BLAST™ (Active Motif, Inc. Carlsbad, California, USA) or NCBI BLAST program...
- Evolution of protein complexes by duplication of homomeric interactions. Jose B Pereira-Leal , Emmanuel D Levy , Christel Kamp and Sarah A Teichmann. Genome Biology 2007, 8:R51
...We used the Smith-Waterman implementation of the TimeLogic's DeCypher® accelerated hardware...
- Gene discovery in Carcinus maenas and Homarus americanus via expressed sequence tags. David W. Towle and Christine M. Smith
Integr. Comp. Biol., Dec 2006; 46: 912 - 918
...blastx mode of Tera-BlastP software on a DeCypher processor Contig ID No. ESTs...sequence versus protein sequence) on a DeCypher server (TimeLogic), with reference to the non-redundant...non-redundant protein database) on a DeCypher processor...
- The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment. Jos Boekhorst, Michiel Wels, Michiel Kleerebezem, and Roland J. Siezen
Microbiology, Nov 2006; 152: 3175 - 3183.
...ncbi.nih.govgenomesBacteria . Sequence similarity was detected by the Smith and Waterman method Smith Waterman, 1981 on a DeCypher hardware-accelerated system Active Motif, Carlsbad, CA. Multiple-sequence alignments were made using Muscle Edgar, 2004 and...
- Changes in Periodontal Health Status Are Associated with Bacterial Community Shifts as Assessed by Quantitative 16S Cloning and Sequencing. Purnima S. Kumar, Eugene J. Leys, Jennifer M. Bryk, Francisco J. Martinez, Melvin L. Moeschberger, and Ann L. Griffen
J. Clin. Microbiol., Oct 2006; 44: 3665 - 3673.
...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...
- What Makes Species Unique? The Contribution of Proteins with Obscure Features. Martin M Gollery, Jeff Jf Harper, John J Cushman, Taliah T Mittler, Thomas T Girke, Jian-Kang Jk Zhu, Julia J Bailey-Serres, and Ron R Mittler.
Genome Biol, Jul 2006; 7(7): R57.
...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.
- Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis.
Mark de Been, Christof Francke, Roy Moezelaar, Tjakko Abee, and Roland J. Siezen.
Microbiology, Oct 2006; 152: 3035 - 3048.
...analysis. HMMER 2.3.2 Durbin et al., 1998 was used for hidden Markov model HMM searches against amino acid sequences and a DeCypher hardware-accelerated system Active Motif was used to perform HMMER searches against nucleic acid sequences. Protein domain...
- A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. Bas E Dutilh , Martijn A Huynen and Berend Snel
Center for Molecular and Biomolecular Informatics / Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen.
BMC Genomics 2006, 7:10 doi:10.1186/1471-2164-7-10.
...
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...
- Zfp312 is required for subcortical axonal projections and dendritic morphology of deep-layer pyramidal neurons of the cerebral cortex
Jie-Guang Chen, Mladen-Roko Rasin, Kenneth Y. Kwan, and Nenad Sestan.
PNAS, Dec 2005; 102: 17792 - 17797.
...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.
- Coiled-coil protein composition of 22 proteomes – differences and common
themes in subcellular infrastructure and traffic control. Annkatrin Rose, Shannon J Schraegle, Eric A
Stahlberg, and Iris Meier. BMC Evol Biol. 2005; 5: 66.
November 16 2005. doi: 10.1186/1471-2148-5-66.
...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...
- Identification of
Candidate Periodontal Pathogens and Beneficial Species by Quantitative
16S Clonal Analysis. Purnima S. Kumar, Ann L. Griffen, Melvin L. Moeschberger, and Eugene J. Leys.J.
Clin. Microbiol., Aug 2005; 43: 3944 - 3955.
... compared to the GenBank database to identify
the closest relatives by using a TimeLogic DeCypher Tera-BLAST server hosted
by the Ohio Supercomputer Center.
- Zfp312 is required
for subcortical axonal projections and dendritic morphology
of deep-layer pyramidal neurons of the cerebral cortex. Jie-Guang Chen, Mladen-Roko Rasin, Kenneth Y. Kwan, and Nenad Sestan. PNAS,
Dec 2005; 102: 17792 - 17797.
... Amino acids alignments were performed by using
the ClustalW algorithm available from DeCypher (http://coe02.ucalgary.ca)
- Structural and functional
characterization of CFE88: Evidence that a conserved and essential
bacterial protein is a methyltransferase. Keith L. Constantine, Stanley R. Krystek, Matthew D. Healy, Michael
L. Doyle, Nathan O. Siemers, Jane Thanassi, Ning Yan, Dianlin
Xie, Valentina Goldfarb,
Joseph Yanchunas, Li Tao, Brian A. Dougherty, and Bennett T.
Farmer, I.
Protein
Sci., Jun 2005; 14: 1472 - 1484.
... Materials and methods
Bioinformatics analysis and threading A DeCypher hardware-accelerated
bioinformatics system (TimeLogic, Inc.) was used to
perform the Smith-Waterman,
FrameSearch, and HMMER searches...
... was used to compare CFE88 with nucleotide sequences from
unfinished microbial genomes, using the DeCypher system as described
in Healy (2003)...
- Databases
and Information Integration for the Medicago truncatula Genome and
Transcriptome. Steven B. Cannon, John A. Crow, Michael L. Heuer, Xiaohong Wang,
Ethalinda K.S. Cannon, Christopher Dwan, Anne-Francoise Lamblin,
Jayprakash Vasdewani, Joann
Mudge, Andrew Cook, John Gish, Foo Cheung, Steve Kenton, Timothy
M. Kunau, Douglas Brown, Gregory D. May, Dongjin Kim, Douglas
R. Cook, Bruce A. Roe,
Chris D. Town,
Nevin D. Young, and Ernest F. Retzel.
Plant Physiology, May 2005; 138: 38 - 46.
... 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. ...
- Structural and functional characterization of CFE88: evidence
that a conserved and essential bacterial protein
is a methyltransferase.Constantine KL, Krystek
SR, Healy MD, Doyle ML, Siemers NO, Thanassi J,Yan N,
Xie D, Goldfarb V, Yanchunas J, Tao L, Dougherty BA, Farmer BT
2nd.
Protein
Sci. 2005 Jun;14(6):1472-84.
Bioinformatics analysis and threading:
A DeCypher hardware-accelerated bioinformatics system (TimeLogic,
Inc.) was used to perform the Smith-Waterman, FrameSearch, and
HMMER searches...
- An
initial strategy for the systematic identification of functional
elements in the human genome by low-redundancy comparative
sequencing. Margulies, Vinson , NISC Comparative
Sequencing Program, Miller, Jaffe, Lindblad-Toh, Chang, Gree,
Lander, Mullikin and Clamp.
Proc.
Natl. Acad. Sci. USA, 10.1073/pnas.0409882102 March 18,
2005
... Matches were detected
with either the BLASTZ computer program (17) or a hardware-optimized
Smith-Waterman algorithm (TimeLogic, Carlsbad, CA)....Smith-Waterman
alignments were generated by using a DeCypher machine (TimeLogic,
Carlsbad, CA)...
- A model of the acid sphingomyelinase
phosphoesterase domain based on its remote structural homolog
purple acid phosphatase.
Marian Seto, Marc
Whitlow, Margaret A. McCarrick, Subha Srinivasan, Ying Zhu,
Rene Pagila, Robert Mintzer, David Light, Anthony Johns, and
Janet A. Meurer-Ogden.
Protein
Sci., Dec 2004; 13: 3172 - 3186.
... With the exception of FASTA,
all database searches were run using TimeLogic DeCypher
- Osprey: a comprehensive tool employing
novel methods for the design of oligonucleotides for DNA sequencing
and microarrays.
Paul M. K. Gordon
and Christoph W. Sensen.
Nucleic
Acids Research, Vol. 32 No. 17
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.
- Computational Identification and Characterization of Novel Genes
from Legume. Michelle A. Graham,
Kevin A.T. Silverstein, Steven B. Cannon, and Kathryn A. VandenBosc.
Plant
Physiology, Jul 2004; 135: 1179 - 1197.
... 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...), which ...
... for Computational Genomics and Bioinformatics at the University
of Minnesota for allowing access to the DeCypher Bioinformatics
Accelerator and for assistance in running analyses...
- Prediction and identification of
Arabidopsis thaliana microRNAs and their mRNA target. Xiu-Jie Wang 1 , José L Reyes , Nam-Hai
Chua and Terry Gaasterland. Genome
Biology 2004, 5:R65
...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...
- Hilary A. M. Lauzon,
Christopher J. Lucarotti, Peter J. Krell, Qili Feng, Arthur
Retnakaran, and Basil M. Ari. Sequence and Organization of the
Neodiprion lecontei Nucleopolyhedrovirus Genome. J.
Virol., Jul 2004; 78: 7023 - 7035.
...Tool (SMART), version 3.4 ( 58 , 59 ), and Smith Waterman
similarity searches using DeCypher with default settings (coe02.ucalgary.ca)...
- Richard L. Eckert, Ann-Marie Broome, Monica
Ruse, Nancy Robinson, David Ryan, and Kathleen Lee S100 Proteins
in the Epidermis
J.
Invest. Dermatol., Jul 2004; 123: 23 - 33.
... The ClustalW sequence comparison
program, http://decypher.stanford.edu/index_by_algo.shtml, was
used to align the protein sequences..
- Li Gan et al. Identification
of Cathepsin B as a Mediator of Neuronal Death Induced by Ab-activated
Microglial Cells Using a Functional Genomics Approach. J.
Biol. Chem., Feb 2004; 279: 5565 - 5572.
... was conducted using a Blast algorithm
against the RefSeq (NCBI) data base on accelerated hardware
(TimeLogic)...
- Martin Madera, Christine
Vogel, Sarah K. Kummerfeld, Cyrus Chothia, and Julian Gough.
The SUPERFAMILY database in 2004: additions and improvements. Nucleic
Acids Res., Jan 2004; 32: 235 - 239.
... Genome assignments Using TimeLogic
DeCypher hardware, the library has been used to carry out assignments
to predicted proteins from ...
- Shuyu Li, Gene Cutler, Jane Jijun Liu, Timothy
Hoey, Liangbiao Chen, Peter G. Schultz, Jiayu Liao, and Xuefeng
Bruce Ling A comparative analysis of HGSC and Celera human genome
assemblies and gene sets. Bioinformatics, Sep 2003; 19: 1597
- 1605.
- Lisa Herron-Olson, John Freeman, Qing Zhang,
Ernest F. Retzel, and Vivek Kapur MGView: an alignment and visualization
tool to enhance gap closure of microbial genomes. Nucleic Acids
Res., Sep 2003; 31: 106. ... 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 ...
- Scott Kroken, N. Louise Glass, John W. Taylor,
O. C. Yoder, and B. Gillian Turgeon. Phylogenomic analysis of
type I polyketide synthase genes in pathogenic and saprobic
ascomycetes. PNAS, Dec 2003; 100: 15670 - 15675.
... 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...
- Healy, M. (2003). Finding Homologs to Nucleic
Acid or Protein Sequences Using the Framesearch Program. Current
Protocols in Bioinformatics. 3.2.1-3.2.23. New York: John
Wiley & Sons, Inc.
- Federico Simone, Roger T. Luo, Paul E. Polak,
Joseph J. Kaberlein, and Michael J. Thirman. ELL-associated
factor 2 (EAF2), a functional homolog of EAF1 with alternative
ELL binding properties. Blood,
Mar 2003; 101: 2355 - 2362.
... 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 ...
- Natalie L. Catlett, Olen C. Yoder, and B.
Gillian Turgeon
Whole-Genome Analysis of Two-Component Signal Transduction Genes
in Fungal Pathogens. Eukaryot. Cell, Dec 2003; 2: 1151 - 1161.
... Conserved Pfam domains were identified
by using the DeCypher hidden Markov model (protein sequence
versus hidden Markov model) search algorithm ...
- Elizabeth H Scholl,
Jeffrey L Thorne, James P McCarter and David Mck Bird. Horizontally
transferred genes in plant-parasitic nematodes: a high-throughput
genomic approach, Genome Biology 2003, 4:R39.
...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...
- Lisa Herron-Olson,
John Freeman1, Qing Zhang, Ernest F. Retzel and Vivek Kapur
MGView: an alignment and visualization tool to enhance gap closure
of microbial genomes. NAR, 2003, Vol. 31, No. 17.
- Sam Griffiths-Jones and Alex Bateman. The
use of structure information to increase alignment accuracy
does not aid homologue detection with profile HMMs. Bioinformatics,
Sep 2002; 18: 1243 - 1249.
... 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....
- G. A. Otto, P. J. Lukavsky, A. M. Lancaster,
P. Sarnow, and J. D. Puglisi. Ribosomal proteins mediate the
hepatitis C virus IRES-HeLa 40S interaction. RNA, Jul 2002;
8: 913 - 923.
... 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
...
- Jing Chen, Yuji Morita, M. Nazmul Huda, Teruo
Kuroda, Tohru Mizushima, and Tomofusa Tsuchiya. VmrA, a Member
of a Novel Class of Na+-Coupled Multidrug Efflux Pumps from
Vibrio parahaemolyticus. J. Bacteriol., Jan 2002; 184: 572 -
576.
... The dendrogram was obtained by using
CLUSTAL W and Decypher of Stanford University computer system
(http://dna.stanford.edu/projects.html)
- Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler,
and Thure Etzold
The EBI SRS server—recent developments. Bioinformatics,
Feb 2002; 18: 368 - 373.
...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 ...
- The
Protein Kinase Complement of the Human Genome
G Manning, DB Whyte, R Martinez, T Hunter, S Sudarsanam (2002).
Science
298:1912-1934 and supplemental
data
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
- Carolyn J. Schultz, Michael P. Rumsewicz,
Kim L. Johnson, Brian J. Jones, Yolanda M. Gaspar, and Antony
Bacic. Using Genomic Resources to Guide Research Directions.
The Arabinogalactan Protein Gene Family as a Test Case
Plant Physiology, Aug 2002; 129: 1448 - 1463.
... 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...
- Science, April 5, 2002, TimeLogic's DeCypher®
Bioinformatics Accelerator and FrameSearch™
algorithm were utilized by Syngenta
to rapidly identify genes within the Syd rice draft genome.
•
Full Text [requires free login]
• Abstract
• Special
Rice Genome Section
- C. Harger, G. Chen, A. Farmer, W. Huang,
J. Inman, D. Kiphart, F. Schilkey, M. P. Skupski, and J. Weller.
The Genome Sequence DataBase.
Nucleic
Acids Res. 28: 31-32.
- Evgeni M. Zdobnov and Rolf Apweiler. InterProScan
– an integration platform for the signature-recognition
methods in InterPro. Bioinformatics
17: 847-848.
- Jonas Anders, Svend Kjær, and Carlos
F. Ibáñez
Molecular Modeling of the Extracellular Domain of the RET Receptor
Tyrosine Kinase Reveals Multiple Cadherin-like Domains and a
Calcium-binding Site
J.
Biol. Chem 276: 35808-35817.
- Beth Borowsky, Nika Adham, Kenneth A. Jones,
Rita Raddatz, Roman Artymyshyn, Kristine L. Ogozalek, Margaret
M. Durkin, Parul P. Lakhlani, James A. Bonini, Sudam Pathirana,
Noel Boyle, Xiaosui Pu, Evguenia Kouranova, Harvey Lichtblau,
F. Yulina Ochoa, Theresa A. Branchek, and Christophe Gerald
Trace amines: Identification of a family of mammalian G protein-coupled
receptors. PNAS
98: 8966-8971
- Chengjun Mo, Jeffrey Suen, Marvin Sommer,
and Ann Arvin
Characterization of Varicella-Zoster Virus Glycoprotein K (Open
Reading Frame 5) and Its Role in Virus Growth J.
Virol. 73: 4197-4207. (chart)
- Craig K. Sherburne, Trevor D. Lawley, Matthew
W. Gilmour, F. R. Blattner, Valerie Burland, Erik Grotbeck,
Debra J. Rose, and Diane E. Taylor
The complete DNA sequence and analysis of R27, a large IncHI
plasmid from Salmonella typhi that is temperature sensitive
for transfer
Nucleic
Acids Res. 28: 2177-2186.
- Mark Waugh, Peter Hraber, Jennifer Weller,
Yihe Wu, Guonghong Chen, Jeff Inman, Don Kiphart, and Bruno
Sobral. The Phytophthora Genome Initiative Database: informatics
and analysis for distributed pathogenomic research.
Nucleic
Acids Res. 28: 87-90.
- Luther E. Lindler, Gregory V. Plano, Valerie
Burland, George F. Mayhew, and Frederick R. Blattner.
Complete DNA Sequence and Detailed Analysis of the Yersinia
pestis KIM5 Plasmid Encoding Murine Toxin and Capsular
Antigen.
Infect.
Immun. 66: 5731-5742.
- DNA Sequencing and Analysis of the Low-Ca2+-Response
Plasmid pCD1 of Yersinia pestis KIM5. Robert D. Perry, Susan
C. Straley, Jacqueline D. Fetherston, Debra J. Rose, Jason Gregor,
and Frederick R. Blattner Infect.
Immun. 66: 4611-4623.
Referencing TimeLogic Products
Please note the following examples
for referencing purposes.
- TimeLogic® DeCypher® (Active
Motif Inc., Carlsbad, CA)
- TimeLogic® GeneDetective™(Active
Motif Inc., Carlsbad, CA)
- TimeLogic® Tera-BLAST™(Active
Motif Inc., Carlsbad, CA)
- TimeLogic® Tera-Probe™ (Active
Motif Inc., Carlsbad, CA)
- TimeLogic® CodeQuest™ (Active
Motif Inc., Carlsbad, CA)
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