AlignmentViewer: Sequence Analysis of Large Protein Families.

Humans Proteins / genetics Sequence Alignment Sequence Analysis, Protein Software Web Browser
JavaScript MSA alignment viewer protein alignments tool web-based

Journal

F1000Research
ISSN: 2046-1402
Titre abrégé: F1000Res
Pays: England
ID NLM: 101594320

Informations de publication

Date de publication:
2020
Historique:
accepted: 12 10 2020
entrez: 2 11 2020
pubmed: 3 11 2020
medline: 2 2 2021
Statut: epublish

Résumé

AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families. The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space. The tool is directly accessible in web browsers without the need for software installation. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, e.g. via EVcouplings.org.

Identifiants

DOI: 10.12688/f1000research.22242.2 PMID: 33123346 PMC: PMC7570326
pubmed: 33123346
doi: 10.12688/f1000research.22242.2
pmc: PMC7570326
pii:
doi:

Substances chimiques

Proteins 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM103504
Pays : United States

Informations de copyright

Copyright: © 2020 Reguant R et al.

Déclaration de conflit d'intérêts

No competing interests were disclosed.

Références

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pubmed: 30304492
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pubmed: 9694995
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pubmed: 26635364
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pubmed: 9632837
PLoS One. 2011;6(12):e28766
pubmed: 22163331
Bioinformatics. 2014 Nov 15;30(22):3276-8
pubmed: 25095880
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W350-5
pubmed: 24848019
Bioinformatics. 2009 May 1;25(9):1189-91
pubmed: 19151095
Bioinformatics. 2016 Nov 15;32(22):3501-3503
pubmed: 27412096

Auteurs

Roc Reguant (R)

Department of Informatics, Technical University of Munich, Munich, Germany.
cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-0350-3899

Yevgeniy Antipin (Y)

Icahn School of Medicine, Mount Sinai, New York, NY, USA.

Rob Sheridan (R)

Knowledge Systems Group, Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Christian Dallago (C)

Department of Informatics, Technical University of Munich, Munich, Germany.
cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0003-4650-6181

Drew Diamantoukos (D)

cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.

Augustin Luna (A)

cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
ORCID: 0000-0001-5709-371X

Chris Sander (C)

cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
ORCID: 0000-0001-6059-6270

Nicholas Paul Gauthier (NP)

cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › AlignmentViewer: Sequence Analysis of Large...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › AlignmentViewer: Sequence Analysis of Large...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Alignement de séquences › AlignmentViewer: Sequence Analysis of Large...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence de protéine › AlignmentViewer: Sequence Analysis of Large...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › AlignmentViewer: Sequence Analysis of Large...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Navigateur › AlignmentViewer: Sequence Analysis of Large...