Pfam: The protein families database in 2021-Reference-Cited by-同舟云学术

Pfam: The protein families database in 2021

Published:2020-10-30 Issue:D1 Volume:49 Page:D412-D419
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Mistry Jaina¹^ORCID,Chuguransky Sara¹^ORCID,Williams Lowri¹^ORCID,Qureshi Matloob¹^ORCID,Salazar Gustavo A¹,Sonnhammer Erik L L²,Tosatto Silvio C E³^ORCID,Paladin Lisanna³^ORCID,Raj Shriya¹^ORCID,Richardson Lorna J¹^ORCID,Finn Robert D¹^ORCID,Bateman Alex¹^ORCID

Affiliation:

1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK

2. Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden

3. Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy

Abstract

Abstract The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this journal, over 350 new families have been added in Pfam 33.1 and numerous improvements have been made to existing entries. To facilitate research on COVID-19, we have revised the Pfam entries that cover the SARS-CoV-2 proteome, and built new entries for regions that were not covered by Pfam. We have reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family. The new Pfam-B is based on a clustering by the MMseqs2 software. We have compared all of the regions in the RepeatsDB to those in Pfam and have started to use the results to build and refine Pfam repeat families. Pfam is freely available for browsing and download at http://pfam.xfam.org/.

Funder

European Union's Horizon 2020 MSCA-RISE action

Wellcome

BBSRC

Open Targets

European Molecular Biology Laboratory Core Funds

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

http://academic.oup.com/nar/article-pdf/49/D1/D412/35363969/gkaa913.pdf

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