workflows - Arabidopsis (Jul/12/2005 )
I'm working on a project that involves creating some complex workflows.
To do this i would have to start with a target gene and find the flanking genes : in Arabidopsis.
1. How would one go about doing that/or finding them.
2. Does any body know of which Bioteam/iNquiry application i can use to get this information
Im copying the following Spec. I would appreciate if any body can comment on how one would go about doing this.
I.Database lookup: Start with a target gene, find flanking genes in Arabidopsis.
II.Blast flanking genes against unigene db (clustered EST database or cDNA db).
III.Blast candidate unigenes back against Arabidopsis genome, eliminate non-syntenic sequences (i.e., eliminate everything with better hits elsewhere in the genome).
IV.Align resulting target unigenes to the genomic sequence with spidey (from NCBI) to identify intron boundaries.
V.Pass results to Primer3 for PCR primer design. The goal is to identify primers that will amplify the introns of the gene identified in step 1.
You can try this adress
or find something on this site (don't care about language, find the link "Arabidopsis.exe" to down load)
hope it is useful for you