Automated selection of homologs to track the evolutionary history of proteins.

ABSTRACT: BACKGROUND:The selection of distant homologs of a query protein under study is a usual and useful application of protein sequence databases. Such sets of homologs are often applied to investigate the function of a protein and the degree to which experimental results can be transferred from one organism to another. In particular, a variety of databases facilitates static browsing for orthologs. However, these resources have a limited power when identifying orthologs between taxonomically distant species. In addition, in some situations, for a given query protein, it is advantageous to compare the sets of orthologs from different specific organisms: this recursive step-wise search might give an idea of the evolutionary path of the protein as a series of consecutive steps, for example gaining or losing domains. However, a step-wise orthology search is a time-consuming task if the number of steps is high. RESULTS:To illustrate a solution for this problem, we present the web tool ProteinPathTracker, which allows to track the evolutionary history of a query protein by locating homologs in selected proteomes along several evolutionary paths. Additional functionalities include locking a region of interest to follow its evolution in the discovered homologous sequences and the study of the protein function evolution by analysis of the annotations of the homologs. CONCLUSIONS:ProteinPathTracker is an easy-to-use web tool that automatises the practice of looking for selected homologs in distant species in a straightforward way for non-expert users.

SUBMITTER: Mier P 

PROVIDER: S-EPMC6245638 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature