Seqrutinator: Scrutiny of Large Protein Superfamily Sequence Datasets for the Identification and Elimination of Non-functional Homologues

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2024 Aug 26

PMID 39187866

Authors

Agustin Amalfitano

Nicolas Stocchi

Hugo Marcelo Atencio

Fernando Villarreal

Arjen Ten Have

Affiliations

Soon will be listed here.

Abstract

Seqrutinator is an objective, flexible pipeline that removes sequences with sequencing and/or gene model errors and sequences from pseudogenes from complex, eukaryotic protein superfamilies. Testing Seqrutinator on major superfamilies BAHD, CYP, and UGT removes only 1.94% of SwissProt entries, 14% of entries from the model plant Arabidopsis thaliana, but 80% of entries from Pinus taeda's recent complete proteome. Application of Seqrutinator on crude BAHDomes, CYPomes, and UGTomes obtained from 16 plant proteomes shows convergence of the numbers of paralogues. MSAs, phylogenies, and particularly functional clustering improve drastically upon Seqrutinator application, indicating good performance.

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