Any Way To Ncbi Blast Multiple Protein Sequences?

Question

[jolespin]

Is there any tools or any direction anyone can point me in towards Blasting multiple amino acid sequences on http://blast.ncbi.nlm.nih.gov/Blast.cgi ?

I could potentially write a script to do this and grab the Top Hits but I wasn't sure if there was an easier way that would save me the trouble.

[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, Since greengene doesn't work anymore I'm asking you guys if there is another method than bacht 20 proteins at time using NCBI blast, I'm searching for a putative antigenic protein for a putative B. anthracis vaccine.

Thanks for your help!

Serena

[Neilfws]

I have moved your question to here as a comment - it was previously posted as an answer, which is not appropriate. You need to create a new post with your question. Please do that in the next day; this comment thread will be deleted.

[Serena]

Sorry for posted in the wrong section! Thank for your suggestion

Answer 1

[JC]

The easy way is to install it locally and use the -remote flag, check http://www.ncbi.nlm.nih.gov/books/NBK1762/

[Neilfws]

Yes, BLASTing multiple query sequences = installing BLAST locally. Time to learn this core skill :)

[jolespin]

i'm going to try and figure out how this works!

Answer 2

[Brett]

Yep the best way is to install local blast http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download.

If you not use to the command prompt (or dont have time to learn the commands), download the older version here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.25/

and use this website here generates exactly what you need to type into you command prompt : http://www.aridolan.com/bbu/bbuintro.aspx

It makes life very simple

(new update to blast means the old commands no longer work thats why I say to use a legacy version)

Answer 3

[youngcsong]

Can't you already BLAST multiple sequences through the web interface? Surely though, I guess depending on the number of sequences you have, you might also consider taking the route, as already been posted in previous answer.

[QVINTVS_FABIVS_MAXIMVS]

NCBI allows you to input multiple sequences as your own database to search a query to

Answer 4

[Xingyu Yang]

You can just copy multiple sequences in fasta format there and run. However, its results might be not that easy to parse and it's very slow.

The better solution is as mentioned above, install it locally.

Answer 5

[prp291]

NCBI itself provide the facility to do btach BLAST. you can paste the sequence (upto 50) in text box and blast it. You can find some other methods HERE or you can use perl script for batch blast from HERE