¥BLAST
stands for Basic Local Alignment Search Tool. It is used to compare a novel
sequence with those contained in nucleotide and protein databases. The
emphasis of this tool is to find regions of sequence similarity. These can
yield clues about the structure and function of this novel sequence, and about
its evolutionary history and homology with other sequences in the database.
¥The
fundamental unit of the BLAST algorithm output is the High-scoring Segment Pair
(HSP). An HSP consists of two sequence fragments of arbitrary but equal length
whose alignment is locally maximal and for which the alignment score meets or
exceeds a threshold or cutoff score. A set of HSPs is defined by two
sequences, a scoring system, and a cutoff score; this set may be empty if the
cutoff score is sufficiently high. In the programmatic implementations of the
BLAST algorithm described here, each HSP consists of a segment from the query
sequence and one from a database sequence.
¥The
approach to similarity searching taken by the BLAST programs is first to look
for similar segments (HSPs) between the query sequence and a database
sequence, then to evaluate the statistical significance of any matches that
were found, and finally to report only those matches that satisfy a
user-selectable threshold of significance.
¥There are 2
main versions of BLAST available at the EBI, namely WU-BLAST2 and
NCBI-BLAST2. These are distinctly different software packages, although they
have a common lineage for some portions of their code, so the two packages do
their work differently and obtain different results and offer different
features.