Scrutineer: a computer program that flexibly seeks and describes motifs and profiles in protein sequence databases

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Abstract
Scrutineer is an interactive, user-friendly program designed to search for motifs, patterns and profiles in the Swissprot, Protein Identification Resource (PIR) or SeqDb protein sequence databases. Basic capabilities include (i) searches for strings of amino acids with multiple choices at a given position; (ii) searches for strings including variable-length segments and delocalized constraints; (iii) searches over subsets of a database or particular regions within each sequence (e.g. N-terminal one-third); (iv) searches involving secondary structure predictions, physicochemical characteristics, and the like; and (v) searches using aligned sequences as targets with various optional weighting schemes. The various search criteria and hits can be combined and complex targets located. Once the data are loaded into virtual memory, all occurrences in PIR release 22.0 (3.7 X 106 amino acids) of a given short string of amino acids (e.g. ahexamer) are found in -36s. Scrutineer can also describe the entire database, user-specified hits, user-defined regions of sequence and all hits. The source code and accompanying manual are being freely distributed.