# About Blimps

## Blimps Searching Program

The Blimps (blocks improved searcher) searching program can be used to search a protein or DNA sequence against a database of blocks, or the reverse. Each block is converted to a position-specific scoring matrix (PSSM). A PSSM has as many columns as there are positions in the block, and 20 rows, one for each amino acid. Each PSSM entry is a numeric score based on the ratio of the observed frequency of an amino acid in a block column to its expected overall frequency in a large protein database. The observed frequencies are weighted for sequence redundancy and pseudo-counts are added to compensate for unobserved amino acids.

During a search, a block is aligned with a sequence at all possible positions and an alignment score is computed by adding the PSSM scores from every column of the block. If the sequence is DNA, BLIMPS translates it in all six reading frames and scores all six translated sequences.

J.G. Henikoff and S. Henikoff, "Blocks Database and Its Applications", Methods in Enzymology (1996) 266:88-105.

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Page last modified August 2003