How can I batch a blast for more than 200 proteins at the same time?

Question

[Serena]

Hi everone! I'm a student looking for a tool like greengene.uml.edu whare I can batch a blast of 300 proteins at once angainst ncbi proteins data base.

Since greengene doesn't work anymore I'm asking if there is another tool similar to greengene, instead of blasting 20 proteins at time using the NCBI blast tool. I'm need this while I'm searching for a putative antigenic protein for a putative B. anthracis vaccine.

Thanks for your help!

Serena

Answer 1

[Renesh]

Use Blast2GO

[Serena]

Thanks a lot!! I'm trying to use this program right now, but I have problem uploading fasta sequences from ncbi protein bioproject, maybe I need to fix something on blast2go? it says that DNA sequences can't be read, but I've been tried to up load sequences from a serch in ncbi protein, how can it be? Probably I miss something on using ncbi database..

[Renesh]

Your 300 sequences should be in fasta format. you do not need to upload database. Its already available there. Its good to go through documentation first. Follow steps:

1. Prepare your query file in fasta format
2. Upload sequences in load sequences (from file drop down menu)
3. Click on blast tab (use suitable program and evalue); as you have protein sequences use blastp against NCBI protein database

[Serena]

Thank you againg for you help! it works now!