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Web Blast Server

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

  • Regular BLAST includes five programs:

      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).

  • PSI/PHI BLAST

      Position Specific Iterated and Pattern Hit Initiated BLAST is constructed (automatically) from a multiple alignment of the highest scoring hits in an initial BLAST search. The PSSM is generated by calculating position-specific scores for each position in the alignment. Highly conserved positions receive high scores and weakly conserved positions receive scores near zero. The profile is used to perform a second (etc.) BLAST search and the results of each "iteration" used to refine the profile. This iterative searching strategy results in increased sensitivity. Visit NCBI for details.

  • Mega 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 details.

  • BLAST 2 sequences

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

Last modified: Tue Mar 18 15:24:44 EDT 2008
Page created: 5 January, 2006 		Maintained by: Jing Yu, CottonDB Curator
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