Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding.

ABSTRACT:

Motivation

The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link seq

SUBMITTER: Chang CH 

PROVIDER: S-EPMC9913046 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature