Wikiomics:Genome annotation - Revision history

Torsten Waldminghaus: add tag

Torsten Waldminghaus — Wed, 27 Feb 2008 11:28:57 GMT

add tag

←Older revision		Revision as of 11:28, 27 February 2008
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	* Bremen pipeline described in [http://www.pnas.org/cgi/content/full/100/14/8298 PNAS]		* Bremen pipeline described in [http://www.pnas.org/cgi/content/full/100/14/8298 PNAS]
	* [http://www.megx.net/jcoast/index.php?navi=about JCOAST ] "java based program for comparative genomics working on top of GenDB v2.2 projects".		* [http://www.megx.net/jcoast/index.php?navi=about JCOAST ] "java based program for comparative genomics working on top of GenDB v2.2 projects".
		+
		+
		+	[[Category:Protocol]] [[Category:In silico]] [[Category:Data analysis]]

Darek Kedra: /* Eukariota, genomic level) */

Darek Kedra — Wed, 20 Feb 2008 18:48:48 GMT

Eukariota, genomic level)

←Older revision		Revision as of 18:48, 20 February 2008
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	"""The Conrad gene caller is tool for predicting gene structures in DNA based on the DNA sequence and other available evidence. The gene caller uses semi-Markov Conditional Random Fields. The Conrad CRF engineis a general purpose CRF engine used by the gene caller to provide the structure and algorithms for gene calling."""		"""The Conrad gene caller is tool for predicting gene structures in DNA based on the DNA sequence and other available evidence. The gene caller uses semi-Markov Conditional Random Fields. The Conrad CRF engineis a general purpose CRF engine used by the gene caller to provide the structure and algorithms for gene calling."""

		+	* SNAP from Ian Korf: ik1@sanger.ac.uk
		+	Korf, Ian. “Gene finding in novel genomes.” BMC Bioinformatics 5, no. 1 (2004): 59.

	===Prokaryots===		===Prokaryots===
	* Bremen pipeline described in [http://www.pnas.org/cgi/content/full/100/14/8298 PNAS]		* Bremen pipeline described in [http://www.pnas.org/cgi/content/full/100/14/8298 PNAS]
	* [http://www.megx.net/jcoast/index.php?navi=about JCOAST ] "java based program for comparative genomics working on top of GenDB v2.2 projects".		* [http://www.megx.net/jcoast/index.php?navi=about JCOAST ] "java based program for comparative genomics working on top of GenDB v2.2 projects".

Darek Kedra: stub

Darek Kedra — Mon, 04 Feb 2008 17:14:14 GMT

stub

New page

{{stub}}
'''Genome annotation''' process of finding functional (genes, regulatory elements, ncRNAs) and non-functional features (repeats) in the genomic sequence.

=Gene finding=
==Comparative==

'''Side issue:''' accurate cross-species genomic alignments
* [http://genserv.anat.ox.ac.uk/grape GRAPe] GRAPe is a tool for computing genome re-alignment using marginalized posterior decoding.

===Eukariota===

* [http://bio.math.berkeley.edu/slam SLAM] [http://nar.oxfordjournals.org/cgi/content/full/31/13/3507 HTML]
* [http://www.tigr.org/software/pirate/twain/twain.html TWAIN] [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1782 HTML]
* [http://www.sanger.ac.uk/Software/analysis/projector/ PROJECTOR @Sanger]
* DOUBLESCAN
* N-SCAN [http://ai.stanford.edu/~serafim/CS374_2005/Papers/CrossSpeciesGeneFinding_NSCAN.pdf PDF]
* AAT
* EVOGENE
* SGP2

* [http://www.plantgdb.org/prj/yrGATE/ yrGATE] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1779557 HTML] Plant comparative genomics
===Prokariota===

* GLIMMER
==de novo==

* [http://cbcb.umd.edu/software/jigsaw/ Jigsaw] meta-program designed to use the output from gene finders, splice site prediction programs and sequence alignments to predict gene models.

===Eukariota, genomic level)===
* [http://augustus.gobics.de/ Augustus] [http://genomebiology.com/2006/7/s1/S11 HTML]
* [http://www.genezilla.org/ GeneZilla]
* [http://www.broad.mit.edu/annotation/conrad/ Conrad] java standalone
"""The Conrad gene caller is tool for predicting gene structures in DNA based on the DNA sequence and other available evidence. The gene caller uses semi-Markov Conditional Random Fields. The Conrad CRF engineis a general purpose CRF engine used by the gene caller to provide the structure and algorithms for gene calling."""

===Prokaryots===
* Bremen pipeline described in [http://www.pnas.org/cgi/content/full/100/14/8298 PNAS]
* [http://www.megx.net/jcoast/index.php?navi=about JCOAST ] "java based program for comparative genomics working on top of GenDB v2.2 projects".