Question: Extract out only subject line from local blast fasta file
gravatar for le.hai
2.7 years ago by
le.hai0 wrote:

Hi I would like to output all the subject line from the alignment with blastn. When I BLAST using NCBI webpage, I can download all the aligned sequences in FASTA form. With this I can later input into my code in R for further analysis. I want to do the same thing with my blastn in windows, where I can extract all the subject line (bolded) in a fasta form.

SSTP_scaffold0000007 length=368211 Length=368211

Score = 46.4 bits (50), Expect = 2e-006 Identities = 25/25 (100%), Gaps = 0/25 (0%) Strand=Plus/Minus




blast R genome • 1.1k views
ADD COMMENTlink modified 2.7 years ago by Sean Davis26k • written 2.7 years ago by le.hai0

Just for others for clarification: you have to do the filtering in Windows? Have you ever tried Cygwin (to use grep)?; linux virtual machine?; or just the basic (and free) EC2 instance from Amazon Web Services?

ADD REPLYlink written 2.7 years ago by Kevin Blighe61k

Hi Kevin, thank you so much for your suggestion, I will look at those options, I initially wanted to do in Windows because I haven't got much experience with Linux and such, but I will make sure to give these a try.

ADD REPLYlink written 2.6 years ago by le.hai0
gravatar for Sean Davis
2.7 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

Do these help you?

ADD COMMENTlink written 2.7 years ago by Sean Davis26k

Hi Sean, thank you! I haven't thought about using blast through R, I initially thought of just editing the blastn output file using simple loop of recognizing the lines with sbjct, but the package seems pretty neat! I will give this a try and post my result later!

ADD REPLYlink written 2.6 years ago by le.hai0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1498 users visited in the last hour