Contents
General
How is TimeLogic affiliated with Active Motif?
The TimeLogic Corporation was purchased by Active Motif in 2003. TimeLogic® is a brand name for the DeCypher® and CodeQuest® product lines.
What technology is used to accelerate your bioinformatics algorithms?
We have taken some very commonly used bioinformatics algorithms and optimized them to run on our FPGA accelerator cards (SeqCruncher™).
How big can I go in building a DeCypher® system?
Since our technology scales with near-linearity, we can easily & quickly add capacity to a system by adding more FPGA cards. Thus, one or more SeqCruncher cards can be installed in a server and/or multiple servers can be chained together to form a multi-node system.
As far as system size limits go, we have yet to reach that upper limit. We have customers with literally dozens of our FPGA cards incorporated into large, multi-node DeCypher® systems.
On these multi-node systems, our DeCypher® software automatically handles job distribution and queueing. End-user communication is via the Master node and the DeCypher® system handles the rest.
What does FPGA mean?
FPGA means field programmable gate array. More Information.
Which algorithms are accelerated?
The various types of BLAST (Tera-BLAST), several implementations of Smith-Waterman (DeCypherSW™), multiple variations of HMM and profile searches (DeCypherHMM™), and GeneDetective (for gene modeling) are supported.
What is the increase in performance using your system?
The DeCypher® and CodeQuest® systems give from 60X - 900X gain in performance based on the specific algorithm and the number of cards in a single server.
What are the key differences between DeCypher® and CodeQuest®?
The DeCypher® system is an enterprise solution that allows for unlimited scalability based on the number of servers you want to use, while CodeQuest® is a plug-and-play workstation that enables you to create a stand-alone one- or two-card system. Whichever hardware configuration is best for your research goals, both solutions use the same SeqCruncher accelerator card and DeCypher® software.
Can the system accept a single sequence query?
Yes. You can submit a search with a single query sequence, but you will see the most dramatic acceleration in performance when you submit hundreds to thousands of sequences.
Hardware
Can the SeqCruncher card be installed in my own server?
In order to ensure the high-quality that we demand for our DeCypher® systems, we thoroughly test the host-servers that we use. As long as your host-server is on our list of tested hardware, and it meets our specifications, it can be used in a DeCypher® system.
We currently support the following servers:
- Dell R710 (2U rackmount server)
- CPUs: 2 quad-core Xeon CPUs (~ 3 GHz)
- RAM: 8-16 GB RAM
- Other: gigabit ethernet
- Storage: 6x146GB storage (minimum)
- Dell R900 (4U rackmount server)
- CPUs: 4-6 quad-core Xeon CPUs (~3 GHz)
- RAM: 24-32 GB RAM
- Other: gigabit ethernet
- Storage: 6x146GB storage (minimum)
- Required Operating Systems:
- RedHat Enterprise v5.2
- CentOS v5.2
- Windows Server 2003
Our SeqCruncher FPGA cards require a PCIe slot (one per card).
Installation of the SeqCruncher card(s) and DeCypher® software require a trained TimeLogic specialist.
Can more than one SeqCruncher card be installed per server?
Yes. The above servers support 1, 2 or 3 SeqCruncher cards for the Dell R710 and 1 - 7 FPGA cards for the Dell R900.
Can the SeqCruncher card and associated DeCypher® software be run in a Linux environment?
Yes. You can also install the card and run the software in a PC Windows or Linux environment.
Can I accelerate my own bioinformatics algorithm with your SeqCruncher card?
No. Our SeqCruncher card is designed to run only DeCypher® software algorithms.
Can I install the command line interface client on my laptop?
Yes. The command line interface client can be installed on any remote machine running a Windows, Linux or Mac OS X environment.
Software
What is DeCypher®?
DeCypher® employs a comprehensive set of ultra-fast analysis tools that let you experiment with varied parameter settings—or completely different algorithms—to define the best possible sequence annotation protocol. DeCypher® features both a web interface & a command line client, enabling all users to execute powerful bioinformatics analyses.
How would I use DeCypher® to predict the function of a gene?
DeCypher® enables you to quickly process comprehensive BLASTX searches of your gene sequences against a well-curated protein database of known proteins. To reinforce your conclusions, it is possible to compare your protein sequence with an annotated Hidden Markov Model database such as PFAM. A match to a specific protein family can imply similar function. DeCypher's HMM-Framesearch method is also available for automatic translation of your nucleic sequences and frameshift tolerant alignments while assigning protein family identification.
Can I use DeCypher® to rapidly identify exons and splice variants?
Yes. The GeneDetective™ algorithm allows you to map ESTs or amino acid sequences to genomic data to build sophisticated gene models. This system uses multiple sequence alignment methods to accurately describe exons and introns, and then it delivers a interactive graphical view of your gene model for exploration of splice variants. Since our accelerated Tera-Blast algorithm is used in this process, your jobs takes much less time than alternative methods require.
Can DeCypher® be used for protein structure modeling?
Yes. For homology modeling, DeCypher®'s BLAST and robust Smith-Waterman methods can be used to find sequences with known protein structure by comparison with protein structure data such as that found in the Protein Data Bank (PDB).
Can DeCypher® be used to identify distantly-related sequences?
Yes. DeCypherHMM™ enables you to build your own Hidden Markov Model database from a collection of similar proteins. This model can then be used to search for remote homologs through comparison with a large sequence database.
Database FTP Download Sites
The following list displays database sources of selected files for creating DeCypher® or CodeQuest® target databases.
| Type | Site | Database Name | Database Description & Notes |
|---|---|---|---|
| Sequence | NCBI | nr | NCBI non-redundant protein database |
| nt | NCBI non-redundant nucleotide database |
||
| Uniprot | swissprot | Uniprot Swiss-Prot protein database |
|
| trembl | Uniprot trEMBL protein database |
||
| HMM | PFAM | pfam-fs | PFAM HMM library, local alignment models |
| pfam-ls | PFAM HMM library, global alignment models |
||
| TIGRFAMs | tigrfam | TIGRFAMs HMM library, standard |
|
| tigrfam-frag | TIGRFAMs HMM library, fragment-mode |
