Species-specific analysis of protein sequence motifs using mutual information

Background: Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions. Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and, in particular, evolutionary features of the underlying sequences. Results: We describe the tool PROfile analysis based on Mutual Information (PROMI) that enables comparative analysis of user-classified protein sequences. PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side. On the client-side platform-indepe...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Jan Hummel, Nima Keshvari, Wolfram Weckwerth, Joachim Selbig
• Keywords: BMCBI 2005, Profile, Protein Sequences, Sequences