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BLAST2: with gaps (Altschul, Madden, Schaeffer, Zhang, Miller, Lipman)

Some explanations about the options

nucleotid db

choose a nucleotide db for blastn, tblastn or tblastx

Blast program

The five BLAST programs described here perform the following tasks:

. blastp compares an amino acid query sequence against a protein sequence database;

. blastn compares a nucleotide query sequence against a nucleotide sequence database;

. blastx compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database;

. tblastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).

. tblastx compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

psitblastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands) using a position specific matrix created by PSI-BLAST.

protein db

Choose a protein db for blastp or blastx.

Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (-e)

The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable.

Sequence format

The sequence will be automatically converted in the format needed for the program

providing you enter a sequence either:

in plain (raw) sequence format or in one of the following known formats:

IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP

You may enter in the text area a database entry code, or an accession number, in this form:

database:entry_name

or:

database:accession.

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