BLAST (short but very famous name) is one of the most popular tool in bioinformatics to find a local optimal alignment for a given sequence. In this post, we will briefly review the classical paper (Altschul et.al 1991) and discuss “what’s going on with BLAST now”.
1. Brief BLAST revisited
We only sketch here the idea of BLAST because Wikipedia described very well. Their ideas are (in a very few words): (i) using k-mers(sometimes called k-tupples or k-letters) for the query sequence, then listing all possible matching (ii) Calculating the so-called high-scoring segment pair (HSP) (iii) Using statistical test for getting the significant matches. (and of course ones whose the small p-value (usually <0.01) will be listed as the local optimal results.
2. Discussion
- Comparison with the similar algorithm FASTA (next post)
- Various BLAST variants : NCBI maintanced a big collection, and the most recent one is Fast-BLAST (appeared in PLoS ONE last month) where they used a heuristic way to indexing the data based on the clusters and alignments from protein families).
- Any comments ?
3. BLAST vs. FASTA
BLAST and FASTA are two famous algorithms in sequence alignment. Between them, there are some similarities and differences
Tags: BLAST
