Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
BLAST+ creating custom blast database and using blast+ filtering features deniz Bioinformatics 3 07-07-2019 09:04 AM
MiSeq Grant Program...apply as SEQanswers? ECO Illumina/Solexa 6 10-12-2012 05:33 AM
attempt to apply non-function while trying DEseq vignette sample data LanaG Bioinformatics 7 10-25-2011 01:19 PM
Transcriptome Unclassified Blast Query Giorgio C Bioinformatics 0 10-28-2010 08:41 AM
How to BLAST a genome against Transcriptome sequence Dalmi RNA Sequencing 3 10-15-2010 03:17 AM

Thread Tools
Old 04-14-2013, 08:58 AM   #1
Location: ND, USA

Join Date: Oct 2011
Posts: 28
Default How? - Apply BLAST identities to transcriptome

Hello, I could use help with the following problem -

I've assembled a transcriptome and I can BLAST against Drosophila to identify some of the transcripts. Now I have two files: the BLAST output and transcript fasta. I would like to append the names (subject IDs) from the BLAST file to the fasta >headers.

The closest I can get is to format my BLAST output to a CSV with the query and subject IDs in the first two columns, but I'm not sure how to put together a script that will search for transcripts in my fasta and add the IDs.

Any advice or other solutions?


Last edited by dacotahm; 04-14-2013 at 09:00 AM.
dacotahm is offline   Reply With Quote
Old 04-15-2013, 03:16 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

Which scripting language are you learning? e.g. Perl, Python, or Ruby.

Whichever you pick, this should be a simple job combining the FASTA input file and the BLAST output to give an annotated FASTA file. BioPerl, Biopython or BioRuby would make it easy to work with the BLAST XML output, but I'd recommend the tabular output as it is trivial to parse.
maubp is offline   Reply With Quote
Old 04-15-2013, 09:33 AM   #3
Location: US

Join Date: Sep 2010
Posts: 14

MAKER comes with an accessory script (maker_functional_fasta) that maps functional information onto a fasta. It might take some shuffling of your BLAST output to get it in the expected input format.
MeganS is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:11 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO