Blastp Against Human Proteome

Question

[Sophie]

Hey guys,

I have a list of gi's for about 10000 protein sequences all from vertebrate species. I want to blast these sequences against non-redundant protein sequences only from humans.

I will run the blast on a local cluster.

Can anyone help me with the appropriate command line that I need to use?

Thanks,

Answer 1

[Darked89]

You may also try http://www.uniprot.org/batch/ (this one has 10k entries limit)

For accession/GI conversion if needed use: http://www.ebi.ac.uk/Tools/picr/

[Sophie]

I tried the ID mapping at Uniprot, however, it managed to map only 60% of the gi's. I'll now give a try with the conversion tool at EBI that you mentioned.

Answer 2

[Sophie]

I broke the problem into the following parts.

1) Get the fasta sequences for all the gi's 2) Create human refseq database (formatdb) 3) blastp -d custom_database -i human_fasta

For the first, I would normally go to Batchz Entrez, submit the list of gi's, and then send the fasta sequences to file. However, this is not working for 10000 gi's. I reduced the number to as low as 500, but NCBI stil does not generate the fasta file and reports an error - "Your session has expired. Please repeat your search".

Any suggestions on how to retrieve this many protein sequences given their NCBI gi's?

[Darked89]

This could be a temporary problem with NCBI servers. I used to download tens of thousands ESTs (using Taxonomy).

[Sophie]

Thanks for the reply, darked89. I have been using the NCBI servers, particularly the Batch Entrez service, for quite a while now and have never experienced such a problem.

I first thought that expired session might be due to submitting too many gi's, but the problem persisted even when I reduced the number to reasonable levels.

Let's hope that it is a temporary server problem.

Do you know any alternative way to retrieve the sequences?

[Jan Kosinski]

You may try idfetch program (http://manpages.ubuntu.com/manpages/dapper/man1/idfetch.1.html) from NCBI tools, which does not impose any limits for number of GIs. On ubuntu, you can get it by installing ncbi-tools-bin package. Alternatively, you can try EUtilities, but I think there were also some limits on number of GIs per request there.