How to extract blast hits sequences in fasta format using BLAST+ running on windows command prompt?

Question

[lev.del.bem]

Hi guys,

I am trying to get the sequences out of a blastp result using the latest release of blast+ (2.6.0) using the windows version on the command prompt. Is there an easy way?

Thanks

Answer 1

[h.mon]

It is not clear what do you mean by "get the sequences out of a blastp result", as you don't say nothing about how you run blast, what kind of output you have, and if you want to retrieve the original subject sequence or only the matching parts between query and subject.

You can use blastdbcmd on windows to retrieve sequences from the database, but there won't be any linux tools (sed, awk, cut, tr, sort, and so on) to help you parse files in caso of need.

If you are using Windows 10, install the Windows Subsystem for Linux, also known as Bash on Ubuntu on Windows.

Answer 2

[theobroma22]

You need to give more information to help you. First, you can use -help in the command line to see how to change the output, like the formatting style. Next, do you have only one result or many results per blast query? Do you want to extract the sequences in the Windows CMD terminal or input the file into R, SAS or other? In summary, there is more than one way to do this, but we need to know the framework you are working under.