find the rest of the sequence - (Aug/25/2004 )

HI

Hi I have a 300b sequence. I want to run this sequence through the whole Zebrafish (Danio rerio) genome.

what can I do

Hi!

Just go to

http://www.ncbi.nlm.nih.gov/genome/guide/z...fish/index.html

and blast your sequence....

mike

thank for your prompt answer but the problem is that the blast dosn't work because this gene was not yet found in fishes (the sequence of the gene that I look for was not cloned yet in fishes). The structure of the gene in fishes is differ from its structure in mamels or other animals SO I CAN NOT RELY ON THOSE SEQUENCES IN ORDER TO PLAN PRIMERS. my idea is to run my sequence on the whole zebrafish genome and by this way to find the other bases for my primers in order to extend my sequence till I get the complete gene.

thanks again

Hi,

Since you have 300bp of the gene of interest, you can use that as a probe to find the gene. I am sure a genomic library for Zebra fish is available. You can do a dot blot to screen the library, and take it from there. BTW, did you even attempt to design a primer for the gene using homologous sequences. Sometimes you get really lucky!

SV