Greedy de novo motif discovery to construct motif repositories for bacterial proteomes.

ABSTRACT:

Background

Bacterial surfaces are complex systems, constructed from membranes, peptidoglycan and, importantly, proteins. The proteins play crucial roles as critical regulators of how the bacterium interacts with and survive in its environment. A full catalog of the motifs in protein families and their relative conservation grade is a prerequisite to target the protein-protein interaction that bacterial surface protein makes to host proteins.

Results

In this paper, we propose a greedy approach to identify conserved motifs in large sequence families iteratively. Each iteration discovers a motif de novo and masks all occurrences of that motif. Remaining unmasked sequences are subjected to the next round of motif detection until no more significant motifs can be found. We demons

SUBMITTER: Khakzad H 

PROVIDER: S-EPMC6471678 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature