Profile-based short linear protein motif discovery.

ABSTRACT:

Background

Short linear protein motifs are attracting increasing attention as functionally independent sites, typically 3-10 amino acids in length that are enriched in disordered regions of proteins. Multiple methods have recently been proposed to discover over-represented motifs within a set of proteins based on simple regular expressions. Here, we extend these approaches to profile-based methods, which provide a richer motif representation.

Results

The profile motif discovery method MEME performed relatively poorly for motifs in disordered regions of proteins. However, when we applied evolutionary weighting to account for redundancy amongst homologous proteins, and masked out poorly conserved regions of disordered proteins, the performance of MEME is equivalent to that of

SUBMITTER: Haslam NJ 

PROVIDER: S-EPMC3534220 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature