automated blast and output
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5.2 years ago
michail • 0

Hi guys, I really hope this question is not too stupid but I just can´t figure it out. 

I have 5 different protein databases from NCBI and a GI list. Now I would like to blast each sequence  from that GI list against those databases and get one fasta file per GI number containing the best hits (but not the query sequence it self) from each of the 5 databases. 

I tried to figure it out with the entrez, efetch, and blast manuals but it does not work at all... 
Can you please help me? 

Thanks a lot in advance.
Michail

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Have you tried the NCBI BLAST+?

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Yes, I did. But I think I mess up the parameters in the command line.

I just started learning how to use command line and the manuals are still a bit difficult to understand sometimes.

So thanks for your patience if I ask weird questions.

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Completely fine. The best way to learn. I would recommend first looking at the manual section on how to use makeblastdb to create a protein database from your protein sequence fast file. If you want to automate the process some and make it work for you I would recommend trying bio python to automate the process some more.

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I figured out how to use the makeblastdb and that worked out for the 5 databases.

Ok, I'll try bio python. thx

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All you should have to do then is use the blast commands and set how you want the output o be parsed.

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