AlignmentViewer: Sequence Analysis of Large Protein Families

Roc Reguant; Yevgeniy Antipin; Rob Sheridan; Christian Dallago; Drew Diamantoukos; Augustin Luna; Chris Sander; Nicholas Paul Gauthier

doi:10.12688/f1000research.22242.2

AlignmentViewer: Sequence Analysis of Large Protein Families

F1000Res. 2020 Mar 27:9:ISCB Comm J-213. doi: 10.12688/f1000research.22242.2. eCollection 2020.

Authors

Roc Reguant^{1

2

3}, Yevgeniy Antipin⁴, Rob Sheridan⁵, Christian Dallago^{1

2

3}, Drew Diamantoukos^{2

3}, Augustin Luna^{2

3

6}, Chris Sander^{2

3

6}, Nicholas Paul Gauthier^{2

3

6}

Affiliations

¹ Department of Informatics, Technical University of Munich, Munich, Germany.
² cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
³ Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
⁴ Icahn School of Medicine, Mount Sinai, New York, NY, USA.
⁵ Knowledge Systems Group, Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
⁶ Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Abstract

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.

Keywords: JavaScript; MSA; alignment viewer; protein alignments; tool; web-based.

Publication types

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

MeSH terms

Humans
Proteins* / genetics
Sequence Alignment*
Sequence Analysis, Protein
Software*
Web Browser

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding