Difference between revisions of "Linking to GEvo"

Revision as of 10:30, 24 August 2009

It's very easy to link into GEvo, which lets you build URLs that specify sequences to be pulled from CoGe's database or from NCBI using an accession. PlantGDB has done this for maize bacs and an example link deconstructed is:

http://synteny.cnr.berkeley.edu/CoGe/GEvo.pl?accn1=Os02g51290;dr1up=50000;dr1down=50000;accn2=Sb04g027950;dr2up=50000;dr2down=50000;gbaccn3=AC190647;num_seqs=3;

(X) refers to the sequence number where the first sequence is 1, the second is 2, the third is 3, etc.

accn(X): retrieve sequence from CoGe's database using an accession. dr(X)up: the amount of sequence to the left of the accession (in base pairs) dr(X)down: the amount of sequence to the right of the accession (in base pairs)

gbaccn(X): the genbank accession to retrieve a sequence from NCBI.

num_seqs=(Y): the number of sequences being submitted

So, the above links specifies three sequences:

• Seq1: database retrieval on name Os02g51290 with 50,000bp to the left and right
• Seq2: database retrieval on name Sb04g027950 with 50,000bp to the left and right
• Seq3: NCBI retrieval for accession AC190647