Gene Prediction Combiner program or software sharing

edge · 01-18-2010, 06:58 PM

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.

strob · 01-18-2010, 11:11 PM

EVidenceModeler (EVM) (http://evidencemodeler.sourceforge.net/)
Jigsaw (http://www.cbcb.umd.edu/software/jigsaw/)

edge · 01-18-2010, 11:58 PM

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.

maubp · 01-19-2010, 03:55 AM

Are you interested in prokaryotes or eukaryotes?

edge · 01-19-2010, 08:30 PM

I will prefer in eukaryotes than prokaryotes...

steven · 01-21-2010, 09:39 AM

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.

edge · 01-21-2010, 08:26 PM

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.

strob · 01-21-2010, 11:28 PM

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....

edge · 01-21-2010, 11:36 PM

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.

strob · 01-21-2010, 11:45 PM

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)

edge · 01-21-2010, 11:54 PM

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 · 01-22-2010, 01:04 AM

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.

steven · 01-25-2010, 11:06 AM

Quote:

Originally Posted by edge

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.

edge · 01-26-2010, 12:20 AM

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 ^^

strob · 01-26-2010, 12:28 AM

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.

edge · 01-26-2010, 12:34 AM

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.

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01-18-2010, 06:58 PM	#1
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	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.

01-18-2010, 11:11 PM	#2
strob Member Location: Belgium Join Date: Nov 2008 Posts: 79	EVidenceModeler (EVM) (http://evidencemodeler.sourceforge.net/) Jigsaw (http://www.cbcb.umd.edu/software/jigsaw/)

01-18-2010, 11:58 PM	#3
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	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.

01-19-2010, 03:55 AM	#4
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Are you interested in prokaryotes or eukaryotes?

01-19-2010, 08:30 PM	#5
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	I will prefer in eukaryotes than prokaryotes...

01-21-2010, 09:39 AM	#6
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	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.

01-21-2010, 08:26 PM	#7
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	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.

01-21-2010, 11:28 PM	#8
strob Member Location: Belgium Join Date: Nov 2008 Posts: 79	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....

01-21-2010, 11:36 PM	#9
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	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.

01-21-2010, 11:45 PM	#10
strob Member Location: Belgium Join Date: Nov 2008 Posts: 79	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)

01-21-2010, 11:54 PM	#11
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	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.

01-22-2010, 01:04 AM	#12
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	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.

01-26-2010, 12:20 AM	#14
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	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 ^^

01-26-2010, 12:28 AM	#15
strob Member Location: Belgium Join Date: Nov 2008 Posts: 79	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.

01-26-2010, 12:34 AM	#16
edge Senior Member Location: China Join Date: Sep 2009 Posts: 199	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.