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workflows - arabidopsis/flanking genes (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 : rolleyes.gif 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.


Hi there

The best method is to go for genomic view for Arabidopsis in NCBI for both of ur gene and flanking gene search and morover there is a separate database for Arabidopsis

Also follow the link below which give u exercise to do ur job well.


Good luck