gVISTA is an automatic server that allows the user to find candidate orthologous regions for a draft or finished DNA sequence from any species on a base genome, and provides detailed comparative analysis.
You can currently align your sequence to the following base genomes: human, mouse, rat, and Drosophila Melanogaster. We are constantly working on expanding the list of base genomes.
gVISTA uses a computational strategy where query sequence contigs are anchored on the base genome by local alignment matches (Kent, 2002) and then globally aligned to candidate regions by AVID program (Couronne et al., 2003, Bray et al., 2003). You will find more details on the strategy in our publication (Couronne et al., 2003).
A sequence up to 300 kilobases long can be submitted by pasting it into a window in plain Fasta format:
- by uploading Fasta file from your computer,
- or by providing GenBank accession number to the server.
After submitting the sequence you receive a link to the computation results. The resulting alignments and detailed comparative analysis of conservation can be viewed via the Vista Browser and its extensions.
In the VISTA Browser you will be able to compare the alignment of your sequence and the genome of your choice to the available precomputed alignments of other species against the same interval of this genome.
For example, if you align your sequence against the human genome, you will see VISTA plots of human/mouse and human/rat alignments along with the alignment of your sequence. If you select D.melanogaster as a base genome, you will see the alignment of D. melanogaster vs D. pseudoobscura together with your alignment.
You can find HELP on VISTA Browser here.