SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
amplicon sequencing on non-model organisms sfyoung Ion Torrent 4 08-29-2013 09:55 AM
SNPdat: Easy annotation of novel and known SNPs from model and non-model organisms d1antho Bioinformatics 0 03-15-2013 08:58 AM
variant effects for non-model organisms chrishah Bioinformatics 2 08-23-2012 02:28 PM
RNA-Seq: Digital gene expression for non-model organisms. Newsbot! Literature Watch 0 08-17-2011 02:00 AM
Genomic enrichment on non-model organisms... MattB General 2 08-08-2008 01:07 AM

Reply
 
Thread Tools
Old 02-12-2014, 12:28 PM   #1
nr23
Member
 
Location: Ireland

Join Date: Oct 2012
Posts: 42
Default Gene Ontology in non-model organisms

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have 2 options:

- BLAST my DE genes against a database with GO terms (human/mouse) to look for orthologs
- Use a program that assigns GO from BLAST results, such as Blast2GO

I've been trying with Blast2GO recently, but find if very slow and generally lacking - does anyone have any experience doing GO in Xenopus or other non-model organisms?

Last edited by nr23; 02-12-2014 at 12:51 PM.
nr23 is offline   Reply With Quote
Old 02-12-2014, 12:41 PM   #2
Birdman
Member
 
Location: Montreal

Join Date: Jan 2014
Posts: 21
Default

I also tried Blast2Go without success using a non-model organism. After countless hours I gave up, since it was messing up my blast results IDs and at the end it was not even retrieving GO terms properly.

Finally, I did the annotation with Trinotate and it went very smoothly. The steps are well described on the website. You need blast results as an input.

Good luck with your analyses.
Birdman is offline   Reply With Quote
Old 04-03-2014, 11:41 PM   #3
amolkolte
Junior Member
 
Location: Pune, India

Join Date: Dec 2012
Posts: 8
Default InterProScan followed by BiNGO

blast2go is on the verge of getting commercialized (as they have started selling PRO versions) and my previous experience was not so good with it. I used IntrProScan to associate GO terms with the transcript sequences. It was a long run but it also reported all the possible sequence features.

To use these custom annotation was tricky for visualization, but thanks to BiNGO, I was able to do it flawlessly. For future use I have documented it here, http://infoplatter.blogspot.in/2014/...alysis-in.html
amolkolte is offline   Reply With Quote
Reply

Tags
gene ontology, rna-seq

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 06:09 PM.


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