prosite pattern to sequences

Question

[mkonstanty]

Hello,

Do you know how to convert a PROSITE pattern into actual list of sequences?

For example, for this pattern: [EQ]-x-L-Y-[DEQST]-x(3,12)-[LIV]-[ST]-Y-x-R-[ST]-[DEQS] I would like to convert to in set a of sequences. . The reason I'd like to have sequences for UniProt Swiss-Prot as there is no possibility to use regex nor prosite pattern.

Answer 1

[Elisabeth Gasteiger]

You can use ScanProsite to obtain the UniProtKB/Swiss-Prot entries that match your pattern, https://prosite.expasy.org/scanprosite/

Use "Option 2 - Submit MOTIFS to scan them against a PROTEIN sequence database."

You can download a command line version of the underlying search engine and run it locally: https://ftp.expasy.org/databases/prosite/ps_scan/