Using the Basic Local Alignment Search Tool (BLAST) Export

@article{citeulike:2363439, abstract = {The BLAST algorithm was developed as a way to perform DNA and protein sequence similarity searches by an algorithm that is faster than FASTA but considered to be equally as sensitive. Both of these methods follow a heuristic (tried-and-true) method that almost always works to find related sequences in a database search, but does not have the underlying guarantee of an optimal solution like the dynamic programming algorithm. FASTA finds short common patterns in query and database sequences and joins these into an alignment. BLAST is similar to FASTA, but gains a further increase in speed by searching only for rarer, more significant patterns in nucleic acid and protein sequences. BLAST is very popular due to its availability on the World Wide Web through a large server at the National Center for Biotechnology Information (NCBI) and at many other sites. The BLAST algorithm has evolved to provide molecular biologists with a set of very powerful search tools that are freely available to run on many computer platforms. This article is intended to be a "user's guide" to the principles underlying BLAST. 10.1101/pdb.top17}, author = {Mount, David W.}, citeulike-article-id = {2363439}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/pdb.top17}, citeulike-linkout-1 = {http://www.cshprotocols.org/cgi/content/abstract/2007/14/pdb.top17}, day = {1}, doi = {10.1101/pdb.top17}, journal = {Cold Spring Harbor Protocols}, keywords = {database, methods, molecular}, month = {July}, number = {14}, pages = {pdb.top17+}, posted-at = {2008-02-11 18:25:10}, priority = {3}, title = {Using the Basic Local Alignment Search Tool (BLAST)}, url = {http://dx.doi.org/10.1101/pdb.top17}, volume = {2007}, year = {2007} }

TY - JOUR ID - citeulike:2363439 L3 - citeulike-article-id:2363439 N2 - The BLAST algorithm was developed as a way to perform DNA and protein sequence similarity searches by an algorithm that is faster than FASTA but considered to be equally as sensitive. Both of these methods follow a heuristic (tried-and-true) method that almost always works to find related sequences in a database search, but does not have the underlying guarantee of an optimal solution like the dynamic programming algorithm. FASTA finds short common patterns in query and database sequences and joins these into an alignment. BLAST is similar to FASTA, but gains a further increase in speed by searching only for rarer, more significant patterns in nucleic acid and protein sequences. BLAST is very popular due to its availability on the World Wide Web through a large server at the National Center for Biotechnology Information (NCBI) and at many other sites. The BLAST algorithm has evolved to provide molecular biologists with a set of very powerful search tools that are freely available to run on many computer platforms. This article is intended to be a "user's guide" to the principles underlying BLAST. 10.1101/pdb.top17 IS - 14 JF - Cold Spring Harbor Protocols TI - Using the Basic Local Alignment Search Tool (BLAST) VL - 2007 SP - pdb.top17 KW - database KW - methods KW - molecular AU - Mount, David PY - 2007/07/01/ UR - http://dx.doi.org/10.1101/pdb.top17 ER -