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, a BLAST search identifies homologous sequences by searching one or more databases usually hosted by NCBI (http://www.ncbi.nlm.nih.gov/), on the query sequence of interest [McGinnis and Madden, 2004].
BLAST is an open source program and anyone can download and change the program code. This has also given rise to a number of BLAST derivatives; WU-BLAST is probably the most commonly used [Altschul and Gish, 1996].
BLAST is highly scalable and comes in a number of different computer platform configurations which makes usage on both small desktop computers and large computer clusters possible.
Subsections
- Examples of BLAST usage
- Searching for homology
- How does BLAST work?
- Which BLAST program should I use?
- Which BLAST options should I change?
- Explanation of the BLAST output
- I want to BLAST against my own sequence database, is this possible?
- What you cannot get out of BLAST
- Other useful resources
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