A list of available sequence annotation tools?

Stegger · 03-04-2009, 01:11 AM

Hi, in reply to a thread here: http://seqanswers.com/forums/showthread.php?t=819 I think it would be great to share tools for annotation of assembled genomes. I have a particular interest in bacteria, but why not make a list of all available tools.

For bacteria I have tried the Manatee annotation service at JCVI:
http://www.jcvi.org/cms/research/pro...vice/overview/

Another tool which I do not have much experience with is The SEED:
http://www.theseed.org/wiki/Main_Page

Suggestion from RudyS: http://www.blast2go.org/

I would greatly appreciate all the links you can provide!

Joann · 03-04-2009, 06:29 AM

For rapidly evolving, up to date focus on genome sequence annotation and comparative genomics, check out the 3rd International Biocuration Conference at

http://projects.eml.org/sdbv/events/...ing/index.html

and do not hesitate to bring forward questions, ideas, suggestions and collaborative projects for all kinds of database annotation strategies.

biblio · 04-13-2012, 11:40 PM

Quote:

Originally Posted by Joann

For rapidly evolving, up to date focus on genome sequence annotation and comparative genomics, check out the 3rd International Biocuration Conference at

http://projects.eml.org/sdbv/events/...ing/index.html

and do not hesitate to bring forward questions, ideas, suggestions and collaborative projects for all kinds of database annotation strategies.

very useful Information for me
thanks

dsenalik · 04-14-2012, 06:34 AM

A new tool released recently ~March 2012 is Mitofy http://dogma.ccbb.utexas.edu/mitofy/ for annotation of plant mitochondrial genomes.
And of course the corresponding tool for plastid genomes that has been available for a while is Dogma http://dogma.ccbb.utexas.edu/

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03-04-2009, 01:11 AM	#1
Stegger Member Location: Copenhagen Join Date: Nov 2008 Posts: 21	List of sequence/genome annotation tools (HELP NEEDED)! Hi, in reply to a thread here: http://seqanswers.com/forums/showthread.php?t=819 I think it would be great to share tools for annotation of assembled genomes. I have a particular interest in bacteria, but why not make a list of all available tools. For bacteria I have tried the Manatee annotation service at JCVI: http://www.jcvi.org/cms/research/pro...vice/overview/ Another tool which I do not have much experience with is The SEED: http://www.theseed.org/wiki/Main_Page Suggestion from RudyS: http://www.blast2go.org/ I would greatly appreciate all the links you can provide! Last edited by Stegger; 03-04-2009 at 01:23 AM.

03-04-2009, 06:29 AM	#2
Joann Senior Member Location: Woodbridge CT Join Date: Oct 2008 Posts: 231	new! International Society for Biocuration For rapidly evolving, up to date focus on genome sequence annotation and comparative genomics, check out the 3rd International Biocuration Conference at http://projects.eml.org/sdbv/events/...ing/index.html and do not hesitate to bring forward questions, ideas, suggestions and collaborative projects for all kinds of database annotation strategies.

04-14-2012, 06:34 AM	#4
dsenalik Carrot Scientist Location: Madison WI USA Join Date: Nov 2009 Posts: 42	A new tool released recently ~March 2012 is Mitofy http://dogma.ccbb.utexas.edu/mitofy/ for annotation of plant mitochondrial genomes. And of course the corresponding tool for plastid genomes that has been available for a while is Dogma http://dogma.ccbb.utexas.edu/