Improving pairwise comparison of protein sequences with domain co-occurrence.

ABSTRACT: Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear wi

SUBMITTER: Menichelli C 

PROVIDER: S-EPMC5766236 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature