The output from a BLAST search consists of four parts. The first is the header (a), which includes the BLAST program and version used, and the name and length of both the query sequence and of the target database. In this case, the program used was BLASTX, so the query sequence was a nucleotide sequence and was translated in all six frames and compared to a protein database, nr, which is the non-redundant protein database maintained by NCBI. The second part of the output (b) is a summary of sequences producing significant alignments, along with both normalized scores and E values (see text for further details; only the four highest-scoring hits are shown). (c) The alignments (MSPs) and their properties are then shown, including the raw score, bit score, E value, and level of identity, for each high-scoring alignment (only one is shown here). (d) Finally, the output includes all of the parameters used in the search, including the scoring matrix used, the penalties used for gaps and extensions, the size of the effective search space (the product of the effective lengths of the query sequence and the database) and the statistical parameters λ and K (only a subset of the parameters are illustrated here).
Pertsemlidis and Fondon Genome Biology 2001 2:reviews2002.1 doi:10.1186/gb-2001-2-10-reviews2002