NCBI Blast Server

NCBI BLAST Server

The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares a nucleotide or protein sequence database to an input set of sequences and calculates the statistical significance of each match. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

blastn - nucleotide sequence against nucleotide database
blastp - amino acid sequence against protein database
blastx - nucleotide (six-frame translation) sequence against protein database;
tblastn - protein sequence against nucleotide database (dynamically translated in all six reading frames).
tblastx - nucleotide (six-frame translation) sequence against nucleotide database (six-frame translations).

CottonGen databases available for BLAST.

Position Specific Iterated and Pattern Hit Initiated BLAST constructs a position-specific scoring matrix (PSSM), or profile, using BLAST matches above a threshold score. The profile is used to perform additional BLAST searches which also refine the profile. This iterative searching strategy results in increased sensitivity and allows for identification of distant evolutionary relationships between proteins. Visit NCBI for more details.
 
CottonGen Databases available for PSI/PHI BLAST.

Mega BLAST uses a greedy algorithm for the nucleotide sequence alignment search. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". When larger word size is used, it is up to 10 times faster than more common sequence similarity programs. Mega BLAST is also able to efficiently handle much longer DNA sequences than the blastn program of traditional BLAST algorithm. Visit NCBI for more details.

CottonGen Databases available for Mega BLAST.

This tool produces the alignment of two given sequences using BLAST engine for local alignment.