Finding homologs to nucleotide sequences using network BLAST searches

Abstract

Basic Local Alignment Search Tool (BLAST) can identify possible homologs in nucleotide and protein databases with high sensitivity and selectivity, and at an amazing speed. Those homologs may provide inference for the biochemical function, the exon boundaries, the domain architecture, the secondary and tertiary structure of the protein, and many other features. The purpose of this unit is not restricted to providing optimal ways of applying the BLAST tool. Just running a BLAST search is an easy task and still can be of great service to researchers. The unit details how to fine tune the arguments of the programs, allowing the user to take advantage of frequently overlooked capabilities of the tool. It also addresses the pitfalls in over- or under-interpretation of results.