Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.

ABSTRACT: A major computational challenge in the genomic era is annotating structure/function to the vast quantities of sequence information that is now available. This problem is illustrated by the fact that most proteins lack comprehensive annotations, even when experimental evidence exists. We previously theorized that embedded-alignment profiles (simply "alignment profiles" hereafter) provide a quantitative method that is capable of relating the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of alignment profiles lies in the interoperability of data format (e.g., alignment information, physio-chemical information, genomic information, etc.). Indeed, we have demonstrated that the Position Specific Scoring Matrices (PSSMs) are an inform

SUBMITTER: Hong Y 

PROVIDER: S-EPMC2962639 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature