SEQanswers

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 08:04 AM
MiSeq Grant Program...apply as SEQanswers? ECO Illumina/Solexa 6 10-12-2012 04:33 AM
attempt to apply non-function while trying DEseq vignette sample data LanaG Bioinformatics 7 10-25-2011 12:19 PM
Transcriptome Unclassified Blast Query Giorgio C Bioinformatics 0 10-28-2010 07:41 AM
How to BLAST a genome against Transcriptome sequence Dalmi RNA Sequencing 3 10-15-2010 02:17 AM

Reply
 
Thread Tools
Old 04-14-2013, 07:58 AM   #1
dacotahm
Member
 
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?

Thanks

Last edited by dacotahm; 04-14-2013 at 08:00 AM.
dacotahm is offline   Reply With Quote
Old 04-15-2013, 02:16 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

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, 08:33 AM   #3
MeganS
Member
 
Location: US

Join Date: Sep 2010
Posts: 14
Default

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.
http://gmod.org/wiki/MAKER_Tutorial_...essory_Scripts
MeganS is offline   Reply With Quote
Reply

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 05:21 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO