I've tried blasting the translated sequence that provides some information, i've looked at the TAIR website (http://www.arabidopsis.org/) and the biofuel feedstock genomics resource which produced phylogenic tree's from Arabidopsis and other related model species
(http://bfgr.plantbiology.msu.edu/index.shtml). But what I'd really like is a website that would allow me just to look at the Arabidposis relatives and produce a phylogenetic tree if any homologues exist. Does anyone know of a high through-put way to do this as I have a long list of genes to investigate.
BioMart has orthologs - you can enter a list of AtG IDs into the Ensembl Plants section and retrieve orthologs in other plant species.
Thanks for the idea Jonathan, is there any advantage to downloading the BioMart software or can all its functions be accessed through the webbrouser? However, i'm more interested in looking for paralogues...
You can get the data from the website without needing the software.
You might find it helpful to use a normal BLAST and then click 'Distance Tree of Results' or 'Taxonomy reports'. These will allow you to see which results are from species that are taxonomically close to Arabidopsis.
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