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| wgVISTA |
About wgVISTAwgVISTA is a set of programs for comparing DNA sequences from two microbial species up to 10 megabases long and visualize these alignments with annotation information ( Frazer et al., 2004, Mayor et al., 2000). It is implemented as an on-line server that provides access to the whole-genome alignment pipeline. The alignment program behind the pipeline is Shuffle-LAGAN, a glocal alignment algorithm that is able to find rearrangements (inversions, transpositions and some duplications) in a global alignment framework (Brudno et al., 2003). The algorithm uses CHAOS local alignments to build a map of the rearrangements between the sequences, and LAGAN to align the regions of conserved synteny. wgVISTA visualization module is the
VISTA Browser,
an interactive Java applet, which is easily configurable, enabling
the visualization of alignments of various lengths at different levels
of resolution. The browser's clean display makes it easy to identify
sequence similarities and differences.
Couronne O., Poliakov A., Bray N., Ishkhanov T., Ryaboy D., Rubin E.,
Pachter L., Dubchak I. 2003. Strategies and Tools for Whole-Genome Alignments.
Genome Research, 13:7. Frazer K.A., Pachter L., Poliakov A., Rubin E.M., Dubchak I.
VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004
Jul 1;32 (Web Server issue):W273-9 Mayor C., Brudno M., Schwartz J.R., Poliakov A., Rubin E.M., Frazer K.A.,
Pachter L.S. and Dubchak I. (2000) VISTA: Visualizing Global DNA Sequence
Alignments of Arbitrary Length. Bioinformatics, 16:1046. Brudno M., Malde S., Poliakov A., Do C.B., Couronne O., Dubchak I.,
and Batzoglou S. Glocal Alignment: Finding Rearrangements During Alignment,
2003. Bioinformatics, 19S1: i54-i62. |