SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Gene prediction with both RNA-seq mapping and genomic sequence based inputs? jstjohn Bioinformatics 3 04-08-2011 11:59 AM
Gene extraction software andreitudor Bioinformatics 1 03-16-2011 01:21 PM
Gene prediction programs that work with multi-fasta files Hobbe Bioinformatics 0 11-16-2010 02:31 AM
AMOS & BAMBUS program experience sharing and general user guide. Patrick Bioinformatics 8 07-08-2010 03:28 PM
PubMed: The effect of sequencing errors on metagenomic gene prediction. Newsbot! Literature Watch 0 11-17-2009 03:10 AM

Reply
 
Thread Tools
Old 01-18-2010, 06:58 PM   #1
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
Default Gene Prediction Combiner program or software sharing

Hi,
Can anyone share about the program or software use for combining gene prediction?
As I know, GLEAN is a gene predictor combiner tool used to generate a single set of gene predictions from a collection of predictions.
Besides that, Combiner is also another similar tools like GLEAN to generate a single set of gene predictions from a collection of gene predictons.
Thanks a lot for sharing.
edge is offline   Reply With Quote
Old 01-18-2010, 11:11 PM   #2
strob
Member
 
Location: Belgium

Join Date: Nov 2008
Posts: 79
Default

EVidenceModeler (EVM) (http://evidencemodeler.sourceforge.net/)
Jigsaw (http://www.cbcb.umd.edu/software/jigsaw/)
strob is offline   Reply With Quote
Old 01-18-2010, 11:58 PM   #3
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
Default

thanks a lot for sharing, strob.
You got experience using the EVM and Jigsaw?
I just try to download the EVM. But it seems like the connection from sourceforge got some problem.
Can't download it successfully.
thanks again.
edge is offline   Reply With Quote
Old 01-19-2010, 03:55 AM   #4
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

Are you interested in prokaryotes or eukaryotes?
maubp is offline   Reply With Quote
Old 01-19-2010, 08:30 PM   #5
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
Default

I will prefer in eukaryotes than prokaryotes...
edge is offline   Reply With Quote
Old 01-21-2010, 09:39 AM   #6
steven
Senior Member
 
Location: Southern France

Join Date: Aug 2009
Posts: 269
Default

EuGène is a gene-finder for eukaryotic sequences annotation. It can integrate pretty much any kind of information, but can also run "ab initio". Already tuned for several plant genomes.
steven is offline   Reply With Quote
Old 01-21-2010, 08:26 PM   #7
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
Default

thanks a lot for your suggestion, steven.
But it seems like can't download successfully from the internet?
It also facing some problem when accessing their website.
edge is offline   Reply With Quote
Old 01-21-2010, 11:28 PM   #8
strob
Member
 
Location: Belgium

Join Date: Nov 2008
Posts: 79
Default

Concerning Eugene, I used to work with Eugene (Ostreococcus genome paper) and I can get you into contact with its main developers or main users....
strob is offline   Reply With Quote
Old 01-21-2010, 11:36 PM   #9
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
Default

Really?
Thanks a lot for your help first.
I just want try to use their software and running it first.
Hopefully it can achieve my desired goal.
edge is offline   Reply With Quote
Old 01-21-2010, 11:45 PM   #10
strob
Member
 
Location: Belgium

Join Date: Nov 2008
Posts: 79
Default

Well, visit this website: http://bioinformatics.psb.ugent.be/
That's my former group where I used to work
Get into contact with Lieven Sterck (see people section). He's the expert concerning annotation and eugene.
You can use my name (steven robbens)
strob is offline   Reply With Quote
Old 01-21-2010, 11:54 PM   #11
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
Default

thanks a lot for your help, steven.
Is it ok that I just said that I'm one of your friend that interested about Eugene software?
The eugene I can't download, right?
It is only web-based usage?
Thanks again and a lot for your help.
edge is offline   Reply With Quote
Old 01-22-2010, 01:04 AM   #12
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
Default

Hi strob,
sorry for troubling you again.
Do you got experience using EVM and Jigsaw before?
Actually I try to explore both of this program as well now.
I try to explore it by using both of the README file and follow their instruction step by step. Unfortunately, it seems like both facing some error message too.
If you don't mind, can I ask for some of your experience using these two program as well?
Thanks a lot.
edge is offline   Reply With Quote
Old 01-25-2010, 11:06 AM   #13
steven
Senior Member
 
Location: Southern France

Join Date: Aug 2009
Posts: 269
Default

Quote:
Originally Posted by edge View Post
thanks a lot for your suggestion, steven.
But it seems like can't download successfully from the internet?
It also facing some problem when accessing their website.
Well, the link to the download section does work but you have to confirm it and add a security exception (don't worry about the secure connection failure).
Alternatively, just drop them an email:
eugene [AT] ossau.toulouse.inra.fr
and/or follow strob's indications (thanks strob!).
cheers,
s.
steven is offline   Reply With Quote
Old 01-26-2010, 12:20 AM   #14
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
Default

Really thanks a lot for your help.
I successfully download it already. I try to install and explore eugene now. Hopefully can perform it successfully soon
In between, do you got experience using this software before?
Is it ok for me to ask me your opinion or advice when I facing problem or question in future?
Thanks a lot for your suggestion first ^^
edge is offline   Reply With Quote
Old 01-26-2010, 12:28 AM   #15
strob
Member
 
Location: Belgium

Join Date: Nov 2008
Posts: 79
Default

I did use it before and as I already explained, we used it in my former lab a lot (Ostreococcus genome papers, poplar genome paper, ectocarpus genome paper, vitis, medicago, ...). But as I left the group almost two years ago, I did not use the tool anymore. But I still have close contacts with my former colleagues, who are still using and refining the tool (together with the people in France). So please do not hesitate to contact Lieven (say that I gave his name). He will be happy to help you further.
strob is offline   Reply With Quote
Old 01-26-2010, 12:34 AM   #16
edge
Senior Member
 
Location: China

Join Date: Sep 2009
Posts: 199
Default

Thanks a lot for your sharing
I will contact Lieven and said that you highly recommend about the Eugene ^^
I trying to explore and installation it now.
Hopefully it is worked perfectly for my research in future.
Thanks again, strob.
edge 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 03:43 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO