SeqTools: visual tools for manual analysis of sequence alignments

BMC Research Notes
Gemma Barson, Ed Griffiths

Abstract

Manual annotation is essential to create high-quality reference alignments and annotation. Annotators need to be able to view sequence alignments in detail. The SeqTools package provides three tools for viewing different types of sequence alignment: Blixem is a many-to-one browser of pairwise alignments, displaying multiple match sequences aligned against a single reference sequence; Dotter provides a graphical dot-plot view of a single pairwise alignment; and Belvu is a multiple sequence alignment viewer, editor, and phylogenetic tool. These tools were originally part of the AceDB genome database system but have been completely rewritten to make them generally available as a standalone package of greatly improved function. Blixem is used by annotators to give a detailed view of the evidence for particular gene models. Blixem displays the gene model positions and the match sequences aligned against the genomic reference sequence. Annotators use this for many reasons, including to check the quality of an alignment, to find missing/misaligned sequence and to identify splice sites and polyA sites and signals. Dotter is used to give a dot-plot representation of a particular pairwise alignment. This is used to identify sequence that...Continue Reading

References

Jun 1, 1994·Computer Applications in the Biosciences : CABIOS·E L Sonnhammer, R Durbin
Apr 29, 2005·BMC Bioinformatics·Erik L L Sonnhammer, Volker Hollich
Aug 24, 2006·Genome Biology·Jennifer HarrowRoderic Guigo
Nov 19, 2009·Nucleic Acids Research·Robert D FinnAlex Bateman
Apr 30, 2010·Database : the Journal of Biological Databases and Curation·Ramana MadupuLinda I Hannick
May 10, 2011·Molecular Biology and Evolution·Jonathan M MudgeJennifer Harrow

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Citations

May 7, 2019·PLoS Neglected Tropical Diseases·Bruno Cesar Bremer HinckelPascal Mertens
Oct 21, 2018·Genome Biology·Emma E DavenportSoumya Raychaudhuri
Sep 25, 2018·Evolutionary Bioinformatics Online·Laurynas KalesinskasCatherine Putonti
Sep 22, 2020·Molecular Phylogenetics and Evolution·Nasim RahmatpourBernard Goffinet

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Software Mentioned

BLAST
Dotlet
MSA
MView
STRAP
SeqTools
SeqView
Sequlator
Jevtrace2
Greyramp

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