Exonerate
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Application data |
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| Created by | Ewan Birney, Guy St C Slater |
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| Principal bioinformatics method(s) | Sequence alignment |
| Technology | Any |
| Created at | European Molecular Biology Laboratory |
| Maintained? | Yes |
| Input format(s) | FASTA |
| Output format(s) | TXT |
| Programming language(s) | C |
| Licence | GPL |
| Operating system(s) | Linux |
Summary: Various forms of alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.
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Description
It uses the C4 dynamic programming library. It is designed to be both general and fast. It can produce either gapped or ungapped alignments, according to a variety of different alignment models. The C4 library allows sequence alignment using a reduced space full dynamic programming implementation, but also allows automated generation of heuristics from the alignment models, using bounded sparse dynamic programming, so that these alignments may also be rapidly generated. Sequence alignments generated using these heuristics will represent a valid path through the alignment model, yet (unlike the exhaustive alignments), the results are not guaranteed to be optimal.
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