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GenCore
Public and proprietary databases containing sequence data are growing exponentially. In order to make the most of this data, many companies are undertaking large scale sequence analysis projects. Introduced in early 1995, GenCore is the first sequence analysis package specifically designed for high throughput environments. The abilities to run hundreds of searches in one command line, work with sequences in all popular formats, and create analysis flows without the need for parsers, are just a few of the features that make GenCore a powerful productivity enhancement tool. As a result, GenCore is the sequence analysis solution of choice for many demanding genomic sites.
GenCore integrates popular and advanced homology searches, as well as additional proprietary sequence analysis tools. GenCore applications can be accelerated by Biocceleration's various hardware and software accelerators, and can also be implemented on a software-only basis.
Better Results
GenCore applications are uniquely designed for sensitive and flexible modeling of biological data. Smith-Waterman applications support different gap-open and gap-extend penalties. Frame+ searches independently model codon and 1-2 base inserts. GeneWise applications (commercially implemented only in GenCore) independently model introns , sequencing errors and codon gaps in both the query and the database. Each of these rigorous algorithms fully supports profile and Hidden Markov Model (HMM) queries.
To ensure high quality results, all applications - including faster but less sensitive heuristic applications such as FastA and BLAST - come with default parameters optimized by biocceleration's research team. Furthermore, GenCore annotates all search results with advanced statistical estimation. Flexibility is, nevertheless, maintained, and advanced users can adjust scores, thresholds, and translation tables.
Proprietary analysis applications, RepEater (for detecting all types of repeats), and GeneHunt (for detecting exons and introns), supplement the GenCore package, enabling users to "clean" genomic data before performing a search.
Inherent Automation
GenCore allows modular construction of multi-stage search strategies through a combination of unique features. Multi-Query enables simultaneous submission of several queries (with a full database or even a set of databases as one query). Data Abstraction Layer allows automatic reading of all popular formats. Search results (output) can be used automatically as queries (input format) for further searches and applications, thereby facilitating multi-stage searching. Hardware Abstraction Layer automatically selects the proper acceleration device. Cutoff Results Threshold allows automated decision flow. Combining state-of-the-art algorithms and unique automation features, GenCore offers today's most comprehensive sequence analysis package for high-throughput environments.
Host Support
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- Linux - x86 Linux, libc-2.3 and aboveSun - Solaris 2.7 and aboveCompaq (HP/DEC) - UNIX 4.0D and above
- SGI - IRIX 6.5 and above
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Homology Search
Rigorous Applications
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- Smith-Waterman (with affine scoring) ProfileSearch/ProfileScan Frame+/Frame+Scan ProFrame+/ProFrame+Scan HMMSearch/HMMScan
- GeneWise/GeneWiseScan
(all based on the OneModel technology)
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Other Utilities
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- Database access utilities
- Hardware access and administration utilities
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Supported Data Formats
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- Genbank, EMBL, SwissProt, Blast binary data, GCG8, GCG9/10, FASTA, NBRF, IG.
Data abstraction layer allows easy addition of new database formats and integration with data servers
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Statistical Methods
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- Pearson's statistical estimation for OneModel and FastA applications
- Altschul & Karlin method for BLAST applications
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Interfaces
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- UNIX command line or (optional) Web (HTML/Java) interface through GenWeb
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