THIS PAGE: describes basic features of pairwise local alignment.

Aligning two long DNA sequences by a systematic site-by-site method, such as dynamic programing , can be demanding on computer time. Although sequences generally have conservative regions relatively easy to identify, such regions might be separated by long variable sequences. Identifying the similar regions in two sequences first and start alignment from such regions, therefore, may speed up the alignment process. One such algorithm developed by Altschul is BLAST, Basic Local Alignment Search Tool. BLAST breaks the sequence into short "words" first, matches such words in one sequence to similar words in the other one. Similarity is scored, and if similarity score exceeds a certain value, the word is extended in either direction.

BLAST was developed to speed up search in large database. When a querry sequence is uploaded in NCBI BLAST homepage, BLAST would search for sequences similar to the querry sequence in the data base. Since databases have grown extremely large, time is critical. Although BLAST is a search tool, searches for similar sequences needs alignment.

Basic ideas of BLAST is listed at NCBI (www), so here we do not discuss that.

next: Using BLAST