LAST
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Application data |
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| Biological application domain(s) | Genomics, Comparative genomics |
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| Principal bioinformatics method(s) | Sequence alignment |
| Created at | Computational Biology Research Center (CBRC) - AIST |
| Maintained? | Yes |
| Input format(s) | FASTA |
| Programming language(s) | C++ |
| Licence | GPLv3 |
Summary: Short read alignment program incorporating quality scores
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Contents
Description
The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed length (e.g. BLAST uses 11-mers). To find these variable-length matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a spaced suffix array (or subset suffix array), analogous to spaced seeds (or subset seeds).
The main difference of LAST from BLAST and similar tools (e.g. BLAT, LASTZ, YASS) is that it copes more efficiently with repeat-rich sequences (e.g. genomes). For example: it can align reads to genomes without repeat-masking, without becoming overwhelmed by repetitive hits.
The main differenceof LAST from read-mapping tools (e.g. BWA, SOAP) is that it can find weak similarities, with many mismatches and gaps.
Features
- Handle big sequence data, e.g: Compare two vertebrate genomes or align billions of DNA reads to a genome
- Indicate the reliability of each aligned column.
- Use sequence quality data properly.
- Compare DNA to proteins, with frameshifts.
- Compare PSSMs to sequences
- Calculate the likelihood of chance similarities between random sequences.
Links
References
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