BLAST Earlier Versions, Basic Local Alignment Sequence Tool, Optimal Global Alignment, Nucleotides, Amino Acid,

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Your Ad Here	BLAST (earlier versions) The most popular tool for searching sequence databases is a package called BLAST (basic local alignment sequence tool). It is based on an algorithm, which is at the core of most on-line sequence search servers. It performs pair-wise comparisons of sequences seeking reasons of local similarity, rather than optimal global alignment with all sequences. The BLAST allows pair-wise DNA-DNA, DNA-protein, protein-protein and protein-DNA alignment using the corresponding databases. For BLAST, users can submit upto 20,000 nucleotides in multi-FASTA format and the program searches the database for similar sequences.
The following programmes can be used: (i) BLASTp compares an amino acid query sequence against a protein sequence database; (ii) BLASTn compares a nucleotide query sequence against a nucleotide sequence database; (iii) BLASTx compares a nucleotide query sequence translated in all reading frames against a protein sequence database; (iv) tBLASTn compares a protein query sequence against a nucleotide database dynamically translated in all reading frames; (v) tBLASTx compares the six frame translations of a nucleotide query sequence against the six frame translations of a nucleotide sequence database (it was used to identify clusters of genes residing in large duplicated segments of Arabidopsis genome);
(vi) BLASTz compares long stretches of nucleotides >2 kb; (vii) BLASTbgp allows use of two new BLAST modes, the first is PHI BLAST, which uses protein motifs, such as those found in PROSITE and other motif databases, to increase the likelihood of finding biologically significant matches, and the second is PSI BLAST, which uses an interactive alignment procedure to detect' weak pattern matches. (viii) bl2seq allows a comparison of two known sequences using the BLASTp and BLASTn programmes.	Your Ad Here

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