Bioinformatics explained: BLAST

BLAST (Basic Local Alignment Search Tool) has become the defacto standard in search and alignment tools [Altschul et al., 1990]. The BLAST algorithm is still actively being developed and is one of the most cited papers ever written in this field of biology. Many researchers use BLAST as an initial screening of their sequence data from the laboratory and to get an idea of what they are working on. BLAST is far from being basic as the name indicates; it is a highly advanced algorithm which has become very popular due to availability, speed, and accuracy. In short, BLAST search programs look for potentially homologous sequences to your query sequences in databases, either locally held databases or those hosted elsewhere, such as at the NCBI ([McGinnis and Madden, 2004].

BLAST can be used for a lot of different purposes. Some of the most popular purposes are listed on the BLAST webpage at the NCBI:

Searching for homology

Most research projects involving sequencing of either DNA or protein have a requirement for obtaining biological information of the newly sequenced and maybe unknown sequence. If the researchers have no prior information of the sequence and biological content, valuable information can often be obtained using BLAST. The BLAST algorithm will search for homologous sequences in predefined and annotated databases of the users choice.

In an easy and fast way the researcher can gain knowledge of gene or protein function and find evolutionary relations between the newly sequenced DNA and well established data.

A BLAST search generates a report specifying the potentially homologous sequences found and their local alignments with the query sequence.