DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets.

ABSTRACT: Proteins that are known only at a sequence level outnumber those with an experimental characterization by orders of magnitude. Classifying protein regions (domains) into homologous families can generate testable functional hypotheses for yet unannotated sequences. Existing domain family resources typically use at least some degree of manual curation: they grow slowly over time and leave a large fraction of the protein sequence space unclassified. We here describe automatic clustering by Density Peak Clustering of UniRef50 v. 2017_07, a protein sequence database including approximately 23M sequences. We performed a radical re-implementation of a pipeline we previously developed in order to allow handling millions of sequences and data volumes of the order of 3 TeraBytes. The modified pipeli

SUBMITTER: Russo ET 

PROVIDER: S-EPMC9621593 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature