comparative annotation tool

NicoBxl · 03-28-2011, 12:29 AM

Hi,

I've a newly sequenced genome and an annotated genome from a very related species.

I'm looking for a way to annotate the newly sequenced genome from the annotated one. So I thought that comparative genomics was a good idea. Anyone know a good program to do this ?

Another idea is to take all the gene sequence ( only the CDS ? ) and align them on the newly sequenced genome to find the ortholog genes ..

Thanks in advance,

N.

shandley · 03-28-2011, 07:48 AM

It might depend on how big your genome is. Have you sequenced a large eukaryotic genome, or are you working with a smaller bacterial or viral genome.

I have used MAUVE to aid in this type of thing (http://gel.ahabs.wisc.edu/mauve/). It will at least give you a roadmap to work with, but might not be as automated as what you are looking for.

Similarly if you are working with a smallish genome the Artemis / ACT (http://www.sanger.ac.uk/resources/software/act/) set of tools might be of some use.

There is an interesting tool called the GATU (Genome Analysis Transfer Utility) which is designed for large DNA genomes. I am not sure if it could be used for viral genomes, but it is an interesting approach and worth taking a look at. Chris Upton hosts it as well as other resources at http://athena.bioc.uvic.ca/.

SAH

NicoBxl · 03-28-2011, 07:49 AM

I'm working on large genome ( Bos Taurus ).

I'll test GATU

shandley · 03-28-2011, 07:56 AM

I would be surprised if GATU worked out of the box for a genome of that size. I was recommending it more as a concept than a true solution. It may be possible to replicate what GATU does or find another tool that handles larger data sets.

But it never hurts to try! You could always break your data down into smaller chunks. The largest sequence I have ever put into it was around 160K.

Good luck!

SAH

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03-28-2011, 12:29 AM	#1
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	comparative annotation tool Hi, I've a newly sequenced genome and an annotated genome from a very related species. I'm looking for a way to annotate the newly sequenced genome from the annotated one. So I thought that comparative genomics was a good idea. Anyone know a good program to do this ? Another idea is to take all the gene sequence ( only the CDS ? ) and align them on the newly sequenced genome to find the ortholog genes .. Thanks in advance, N.

03-28-2011, 07:48 AM	#2
shandley Member Location: Saint Louis, MO Join Date: Sep 2010 Posts: 58	It might depend on how big your genome is. Have you sequenced a large eukaryotic genome, or are you working with a smaller bacterial or viral genome. I have used MAUVE to aid in this type of thing (http://gel.ahabs.wisc.edu/mauve/). It will at least give you a roadmap to work with, but might not be as automated as what you are looking for. Similarly if you are working with a smallish genome the Artemis / ACT (http://www.sanger.ac.uk/resources/software/act/) set of tools might be of some use. There is an interesting tool called the GATU (Genome Analysis Transfer Utility) which is designed for large DNA genomes. I am not sure if it could be used for viral genomes, but it is an interesting approach and worth taking a look at. Chris Upton hosts it as well as other resources at http://athena.bioc.uvic.ca/. SAH

03-28-2011, 07:49 AM	#3
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	I'm working on large genome ( Bos Taurus ). I'll test GATU

03-28-2011, 07:56 AM	#4
shandley Member Location: Saint Louis, MO Join Date: Sep 2010 Posts: 58	I would be surprised if GATU worked out of the box for a genome of that size. I was recommending it more as a concept than a true solution. It may be possible to replicate what GATU does or find another tool that handles larger data sets. But it never hurts to try! You could always break your data down into smaller chunks. The largest sequence I have ever put into it was around 160K. Good luck! SAH