GenDBWiki/FeatureTable - Revision history

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2011-10-26T06:15:02Z

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imported>JomunaChoudhuri at 09:50, 19 October 2004

2004-10-19T09:50:39Z

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imported>JomunaChoudhuri at 09:49, 19 October 2004

2004-10-19T09:49:44Z

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imported>JomunaChoudhuri at 09:49, 19 October 2004

2004-10-19T09:49:16Z

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imported>AlexanderGoesmann at 12:11, 14 October 2004

2004-10-14T12:11:54Z

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	= GenDB Features =		= GenDB Features =

	The open source genome annotation system GenDB is based on a relational database management system. Contig sequences can be imported and after predicting the coding sequences (CDS), a number of standard bioinformatics tools like Blast, Pfam, [[InterPro]] etc. can be run on these regions as a basis for the functional (manual) annotation. By storing only a minimal required subset of each tool result (e.g. only a short description and a computed score) and recomputing the complete result (e.g. an alignment) on demand, the storage requirements can be reduced enormously.		The open source genome annotation system GenDB is based on a relational database management system. Contig sequences can be imported and after predicting the coding sequences (CDS), a number of standard bioinformatics tools like Blast, Pfam, InterPro etc. can be run on these regions as a basis for the functional (manual) annotation. By storing only a minimal required subset of each tool result (e.g. only a short description and a computed score) and recomputing the complete result (e.g. an alignment) on demand, the storage requirements can be reduced enormously.

	The software has an object-oriented application programmers interface (API) implemented in Perl which has been partially generated automatically with O2DBI. The latter creates an object-relational mapping onto SQL tables. GenDB has a web frontend and a Gtk user interface that creates dynamic visualizations and can be used for annotating genes based on the computed tool results.		The software has an object-oriented application programmers interface (API) implemented in Perl which has been partially generated automatically with O2DBI. The latter creates an object-relational mapping onto SQL tables. GenDB has a web frontend and a Gtk user interface that creates dynamic visualizations and can be used for annotating genes based on the computed tool results.

	The system features the concept of wizards which		The system features the concept of wizards which are software agents that automate complex repetitive tasks (e.g. ORF editor, frame-shift correction, contig update, etc.). In addition to a search interface, the software can generate statistical plots and includes a virtual 2D gel. The data contained in GenDB can be exported into widely used output formats like FASTA, EMBL, [http://www.sanger.ac.uk/Software/formats/GFF GFF] (genome feature format), and others. An integrated pathway module supports the analysis and visualization of annotated enzymes based on the KEGG metabolic pathways and the PathFinder software.
	are software agents that automate complex repetitive tasks (e.g.~ORF editor,
	frame-shift correction, contig update, etc.). In addition to a search
	interface, the software can generate statistical plots and includes a virtual
	2D gel. The data contained in ~~\gendb{}~~ can be exported into widely used output
	formats like ~~\fasta~~, EMBL, ~~GFF (genome feature~~
	~~format\footnote{\URL~~[http://www.sanger.ac.uk]{/Software/formats/GFF}}), and
	others. An integrated pathway module supports the
	analysis and visualization of annotated enzymes based on the
	KEGG~~~\cite{kegg:2000}~~ metabolic pathways and the [[PathFinder~~]]~\cite{PATHFINDER}~~
	software.

imported>AlexanderGoesmann at 12:03, 14 October 2004

2004-10-14T12:03:14Z

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Unknown user at 00:00, 1 January 1970

1970-01-01T00:00:00Z

New page

__NOTOC__
= GenDB Features =

The open source genome annotation system GenDB is based on a relational database management system. Contig sequences can be imported and after predicting the coding sequences (CDS), a number of standard bioinformatics tools like Blast, Pfam, [[InterPro]] etc. can be run on these regions as a basis for the functional (manual) annotation. By storing only a minimal required subset of each tool result (e.g. only a short description and a computed score) and recomputing the complete result (e.g. an alignment) on demand, the storage requirements can be reduced enormously.

The software has an object-oriented application programmers interface (API) implemented in Perl which has been partially generated automatically with O2DBI. The latter creates an object-relational mapping onto SQL tables. GenDB has a web frontend and a Gtk user interface that creates dynamic visualizations and can be used for annotating genes based on the computed tool results.

The system features the concept of wizards which
are software agents that automate complex repetitive tasks (e.g.~ORF editor,
frame-shift correction, contig update, etc.). In addition to a search
interface, the software can generate statistical plots and includes a virtual
2D gel. The data contained in \gendb{} can be exported into widely used output
formats like \fasta, EMBL, GFF (genome feature
format\footnote{\URL[http://www.sanger.ac.uk]{/Software/formats/GFF}}), and
others. An integrated pathway module supports the
analysis and visualization of annotated enzymes based on the
KEGG~\cite{kegg:2000} metabolic pathways and the [[PathFinder]]~\cite{PATHFINDER}
software.