ps_scan

ps_scan scans protein sequences against PROSITE patterns, rules, and profiles to identify conserved motifs and domains.

Key Features:

• Perl implementation: Implemented in Perl to perform PROSITE-based sequence scanning.
• Complete PROSITE syntax and rules: Implements the full PROSITE patterns, rules, and profiles as defined by the PROSITE database.
• Versatile input formats: Accepts Swiss-Prot and FASTA formatted sequence files.
• External program integration: Invokes PFTOOLS' pfscan for profile-based scanning and psa2msa to generate multiple sequence alignments (e.g., using the "-o msa" output format).
• Reference implementation: Serves as a reference implementation for scanning PROSITE patterns, rules, and profiles against protein sequences.

Scientific Applications:

• Protein family analysis: Identification of conserved domains and motifs across proteins using PROSITE definitions.
• Pattern recognition: Detection of PROSITE-defined sequence patterns and rules indicative of functional or structural features.
• Data integration: Integration of PROSITE pattern, rule, and profile matches with other bioinformatics analyses and databases.

Methodology:

Scans sequences using the PROSITE pattern/rule/profile matching implemented in Perl and calls PFTOOLS' pfscan for profile scanning and psa2msa for producing multiple sequence alignments (e.g., with the "-o msa" output option).