PASS
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Application data |
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| Principal bioinformatics method(s) | Sequence alignment |
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| Maintained? | Maybe |
| Programming language(s) | C++ |
| Operating system(s) | Linux, Windows |
Summary: PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of seed" words (typically 11-12 bases) as well as an index of the precomputed scores of short words (typically 7-8 bases) aligned against each other.
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