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.

• Katari, M. S., Balija V, Wilson RK, Martienssen RA, McCombie WR. Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res. 2005 Apr;15(4):496-504.
  
• Brenner ED, Katari MS, Stevenson DW, Rudd SA, Douglas AW, Moss WN, Twigg RW, Runko SJ, Stellari GM, Richard MW, Coruzzi GM. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics. 2005 Oct 15;6(1):143.
  
• Brenner ED, Stevenson DW, McCombie RW, Katari MS, Rudd SA, Mayer KF, Palenchar PM, Runko SJ, Twigg RW, Dai G, Martienssen RA, Benfey PN, Coruzzi GM. Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biol. 2003;4(12):R78.

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