Blast your sequence against OrthoMaM CDS or EXONS markers using BLAST2

The result is a list of links to matching marker description files and alignments

blastn: nucleotide query / nucleotide db tblastn: protein query / translated nucleotide db tblastx: nucleotide query transl. / transl. nucleotide db psitblastn: protein query / transl. nucleotide db Blast program

Sequence (format)

OrthoMam human CDS: base nt OrthoMam human EXONS: base nt nucleotide db
Expect: upper bound on the expected frequency of chance occurrence of a set of HSPs (E-value)

Query strand to search against database (for blastn, blastx or tblastx) (-S) ? 1: top 2: bottom 3: both

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Some explanations about the options

nucleotide 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 must be in the fasta format !

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References:

Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaeffer,Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402.