Alignment of Biological Sequences with Jalview
James B Procter(University of Dundee), G. Mungo Carstairs(University of Dundee), Ben Soares(University of Dundee), Kira Mourão(University of Dundee), T. Charles Ofoegbu(University of Dundee), Daniel L. Barton(University of Dundee), Lauren Michelle Lui(University of Dundee), Anne Menard(Kitware (United States)), Natasha Sherstnev(Université Paris-Sud), David Roldan-Martinez(Capgemini (France)), Suzanne Duce(University of Dundee), David Martin(University of Dundee), Geoffrey J. Barton(University of Dundee)
Cited by 206Open Access
Abstract
In this chapter, we introduce core functionality of the Jalview interactive platform for the creation, analysis, and publication of multiple sequence alignments. A workflow is described based on Jalview's core functions: from data import to figure generation, including import of alignment reliability scores from T-Coffee and use of Jalview from the command line. The accompanying notes provide background information on the underlying methods and discuss additional options for working with Jalview to perform multiple sequence alignment, functional site analysis, and publication of alignments on the web.
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