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Pfam: The protein families database in 2021.
Mistry, Jaina; Chuguransky, Sara; Williams, Lowri; Qureshi, Matloob; Salazar, Gustavo A; Sonnhammer, Erik L L; Tosatto, Silvio C E; Paladin, Lisanna; Raj, Shriya; Richardson, Lorna J; Finn, Robert D; Bateman, Alex.
  • Mistry J; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Chuguransky S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Williams L; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Qureshi M; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Salazar GA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Sonnhammer ELL; Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden.
  • Tosatto SCE; Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy.
  • Paladin L; Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy.
  • Raj S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Richardson LJ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Finn RD; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Bateman A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
Nucleic Acids Res ; 49(D1): D412-D419, 2021 01 08.
Article in English | MEDLINE | ID: covidwho-894614
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/.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Proteins / Computational Biology / Proteome / Databases, Protein Type of study: Observational study Limits: Animals / Humans Language: English Journal: Nucleic Acids Res Year: 2021 Document Type: Article Affiliation country: Nar

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Proteins / Computational Biology / Proteome / Databases, Protein Type of study: Observational study Limits: Animals / Humans Language: English Journal: Nucleic Acids Res Year: 2021 Document Type: Article Affiliation country: Nar