SAPA is a web-application for searching target sequences in proteins selected by amino acid composition, amino acid profiles and motifs.
Functional modules within proteins follow often a consensus sequence pattern representing a linear sequence motif, however, other regions may only be described by features independent of a distinct sequence pattern like amino acid composition, similarities to scaled profiles of amino acid properties or content of randomly distributed short sequence motifs.
The SAPA-Tool allows the user to specify settings for all this properties additionally to a set of distinct sequence patterns and rules, which allows searching for target regions within one or more proteins fitting to all of the specified properties. The found target regions are sorted on a combined score and offered for download as a FASTA sequence or spreadsheet file. The user may scan a single sequence for target regions or extract a subset of target-containing proteins from a whole proteome.
A paper for this tool is in preparation.
Using PROSITE patterns from the PROSITE database requires a licence for commercial users.