Motif-Aware PRALINE: Improving the alignment of motif regions.

ABSTRACT: Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved sequence motifs is still difficult to achieve, due to the fact that the contribution of these typically short fragments is overshadowed by the rest of the sequence. Here we extended the PRALINE multiple sequence alignment program with a novel motif-aware MSA algorithm in order to address this shortcoming. This method can incorporate explicit information about the presence of externally provided sequence motifs, which is then used in the dynamic programming step by boosting the amino acid substitution matrix towards the motif. The strength of the boo

SUBMITTER: Dijkstra M 

PROVIDER: S-EPMC6233922 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature