User:Jarle Pahr/BLAST

Notes on NCBI's Basic Local Alignment Search Tool (BLAST) software suite:

Algorithms

Nucleotide blast

blastn:

megablast

Protein blast

BLASTp

Psi-BLAST

Delta-BLAST

Other

blastx: blastx is used to search a protein database using a translated nucleotide sequence query.

tblastn: tblastn is used to search a translated nucleotide database using a protein sequence query.

tblastx: tblastx is used to search a translated nucleotide database using a translated nucleotide sequence query.

Primer-BLAST

Bibliography:

Ian Korf: BLAST: http://www.amazon.com/dp/0596002998/ref=rdr_ext_tmb

Tips

Selecting a different algorith may be the difference between a hit and a "no significant similarity found" result. If no significant similarity is found at first attempt, try several algorithms.

Bibliography

http://www.nature.com/scitable/topicpage/basic-local-alignment-search-tool-blast-29096