Recent BLAST Enhancements, New BLAST Features

The BLAST home page has been restructured so that searches using the principal varieties of BLAST— blastn for nucleotides and blastp for proteins—are separated from those involving the translation of a DNA sequence—blastx, tblastn, and tblastx. Special BLAST pages that use pre-set parameters optimized for finding short nucleotide or short peptide matches have also been created. MegaBLAST offers an alternative to blastn large nucleotide queries or batches of multiple query sequences.

Another important enhancement to the BLAST service is the ability to limit searches to a database subset defined by an Entrez query. For example, to limit a blastp search to viral capsid proteins, enter the following query into the new “Limit by Entrez query” box: Viruses [Organism] AND capsid [Protein Name]

To facilitate searches using unique parameter sets, custom parameters for BLAST searches may be saved within a BLAST URL, then book-marked. Choose the desired parameters on the BLAST page, press the Get URL button, and a link to a new page with your parameters set in the URL will be generated.As a new output option, XML has now been added to HTML, PlainText, and ASN.1.

Web PSI-BLAST has been enhanced to accept a Position Specific Score Matrix (PSSM) that can be pasted into the upload box. A reciprocal output option returns PSI-BLAST results as a PSSM, rather than a sequence alignment. The “bioseq” format returns results in the ASN.1 format.

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