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SeqTools: visual tools for manual analysis of sequence alignments.

Gemma Barson¹, Ed Griffiths²

¹Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. gb10@sanger.ac.uk.

BMC Research Notes

|January 24, 2016

Summary

The SeqTools package offers essential tools like Blixem, Dotter, and Belvu for detailed sequence alignment analysis. These standalone tools enhance manual annotation processes for gene models and alignments.

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Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Manual annotation is critical for creating high-quality reference alignments and annotations.
Detailed viewing of sequence alignments is necessary for annotators.
The SeqTools package, rewritten from AceDB, offers standalone tools for sequence alignment visualization and analysis.

Purpose of the Study:

To introduce the SeqTools package, comprising Blixem, Dotter, and Belvu, as standalone tools for sequence alignment analysis.
To highlight the unique functionalities of these tools in supporting manual annotation processes.

Main Methods:

Blixem: A many-to-one pairwise alignment browser displaying multiple sequences against a reference.
Dotter: A graphical dot-plot viewer for single pairwise alignments.
Belvu: A multiple sequence alignment viewer, editor, and phylogenetic tool.

Main Results:

Blixem aids in assessing alignment quality, identifying sequence errors, and locating splice/polyA sites.
Dotter helps identify unrepresented/misrepresented sequence and compare gene models with supporting evidence.
Belvu facilitates analysis of conservation patterns and manual/automatic processing of multiple sequence alignments.

Conclusions:

SeqTools provides unique and essential functionalities for analyzing sequence alignments during manual annotation.
These tools are vital for ensuring the quality of reference alignments, which are foundational for automatic alignment generation.