Larger Word Size in Modified Algorithm Speeds Up BLASTP, BLASTX, TBLASTN Search

Larger Word Size in Modified Algorithm Speeds Up BLASTP, BLASTX, TBLASTN Search. NLM Tech Bull. 2015 Sep-Oct;(406):b11.

[Editor's Note: This is a reprint of an announcement from the National Center for Biotechnology Information (NCBI). To automatically receive the latest news and announcements regarding major changes and updates to NCBI resources and tools please see the subscribe page.]

The NCBI BLAST Web page now offers faster BLASTP, BLASTX, and TBLASTN searches due to a modified algorithm that can use a larger word size. This improvement can make search 2-4 times faster without changing the results most of the time.

Note: You may also recover the search's previous behavior by changing the word size from 6 to 3. To do so, expand "Algorithm parameters" at the bottom of the BLAST page and use the Word size menu.

For more information on the modified algorithm, please see: http://www.ncbi.nlm.nih.gov/pubmed/17921491.