I need to retrieve about 1000 hits from the GenBank to use for my analysis.
if you're performing blast on ncbi site, you won't get more than 500. I'd suggest you run the blast using stand alone versions of the software on a linux terminal, you'll get a lot of results.
Step 1: download the genbank database from ncbi ftp site.
step 2: download the stand alone version of blast from the same site.
step3: prepare a multiple fasta file of your sequences to be analyses.
step4: run blast.
Dear Chantal,
In the algorithm parameters
1.Set the Max target sequences to 5000
2. Set Expect threshold to 15
Thanks to you all. Bharath I was able to get it, I just changed the parameters as you suggested.
The other issue I have is how to get the FASTA format of the 1000 hits. I am able to retrieve for 100 hits at once when i check all and change the display in Genbank to FASTA (text) but not for 1000. Any suggestions?
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