KISSa: a strategy to build multiple sequence alignments from pairwise comparisons of very closely related sequences
Date
2009-01-29
Authors
Marass, Francesco
Journal Title
Journal ISSN
Volume Title
Publisher
BMC Research Notes
Abstract
Background:
The volume of viral genomic sequence data
continues to increase rapidly. This is
especially true for the smaller RNA viruses, which
are relatively easy to sequence in large numbers.
The data volumes cause a number of significant problems for research applications that require
large multiple alignments of essentially complete genomes, which are of the order of 10 kb.
Findings:
We present a simple strategy to enable the creation of large quasi-multiple sequence
alignments from pairwise alignment data. This
process is suitable for large, closely related
sequences such as the polyproteins
of dengue viruses, which need the insertion of very few indels.
Conclusion:
The quasi-multiple sequence alignments gene
rated by KISSa are sufficiently accurate
to support tree-based genome selection for interactive bioinformatics analysis tools. The speed of
this process is critical to providing
an interactive experience for the user.
Description
Keywords
Citation
Marass, F. and C. Upton BMC Research Notes 2009, 2 :91