Viewer for Comparing Genomes to Arabidopsis

NYPG Consortium Phylogenomics Tools

    Comparative Genomics is a useful way of improving annotation of model genomes such as Arabidopsis. Genomic Sequences and ESTs (Expressed Sequence Tags) from several different species are aligned to the Arabidopsis Genome and Protein databases using several different versions of BLAST. Top matches of the blast results are stored here.

    Vicogenta is a web interface used to query the results. The user can view a list of all alignments from a specific gene or region in the genome. User can also determine which Arabidopsis genes match ESTs from the species selected by the user. Use the pull down menu to see list of current databases available.

    GMOD (Generic Model Organism Database) and Gbrowse (Generic Genome Browser) were the Database and Viewer used to display the BLAST alignments and genome annotations. A plugin has been created which allows the user to jump from the browser to Vicogenta. Use the pull-down menu to see a list of GMOD database and viewers available.

    There is also a Blast form that allows the user to align a query sequence to the databases available.

The following publications have used Vicogenta:

    If you have any questions or comments, please contact Manpreet S. Katari Source code is available upon request.

This material is based upon work supported by the National Science Foundation under grant # 0346436

Disclaimer : Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflct the views of the National Science Foundation (NSF)