ProMeTraWiki/GenomeMaps - Revision history

Alu: /* GenomeMaps in ProMeTra */

2012-03-21T09:09:20Z

GenomeMaps in ProMeTra

← Older revision		Revision as of 11:09, 21 March 2012
Line 6:		Line 6:
	Please see the following example of a GenomeMap for clarity:		Please see the following example of a GenomeMap for clarity:

	[[~~Image~~:~~ProMeTraWiki$$GenomeMaps$genomemap~~.png]]		[[File:GenomeMaps_genomemap.png]]

Alu at 15:24, 20 March 2012

2012-03-20T15:24:55Z

← Older revision		Revision as of 17:24, 20 March 2012
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	__NOTOC__		__NOTOC__
	= [[GenomeMaps]] in [[ProMeTra]] =		= GenomeMaps in ProMeTra =

	The replicons of prokaryotic genomes present in the NCBI genome database (as of Dez. 2008)		The replicons of prokaryotic genomes present in the NCBI genome database (as of Dez. 2008) have been converted into so called GenomeMaps for the ProMeTra web interface. A GenomeMap in the ProMeTra context is a SVG based representation of the coding sequences (CDS) identified and annotated in the GenBank files of the individual prokaryotic database entries. GenomeMaps represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name). The order of the CDSs in the Grid representation is determined by the basenumber of the stop codon counted from the origin of replication. The grid is filled by row, i.e. the first CDS is in first row, first column, the second CDS is located at first row second column and so forth. A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates the location on the reverse strand.
	have been converted into so called GenomeMaps for the ProMeTra web interface.
	A GenomeMap in the ProMeTra context is a SVG based representation of the coding sequences (CDS) identified and annotated in the GenBank files of the
	individual prokaryotic database entries. GenomeMaps represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).
	The order of the CDSs in the Grid representation is determined by the basenumber of the stop codon counted from the origin of replication.
	The grid is filled by row, i.e. the first CDS is in first row, first column, the second CDS is located at first row second column and so forth.
	A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates the location on the reverse strand.

	Please see the following example of a GenomeMap for clarity:		Please see the following example of a GenomeMap for clarity:

	[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]		[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]

Admin: 5 revisions

2011-10-26T06:16:37Z

5 revisions

← Older revision	Revision as of 08:16, 26 October 2011
(No difference)

imported>HeikoNeuweger at 14:04, 13 March 2009

2009-03-13T14:04:55Z

← Older revision		Revision as of 16:04, 13 March 2009
Line 6:		Line 6:
	A GenomeMap in the ProMeTra context is a SVG based representation of the coding sequences (CDS) identified and annotated in the GenBank files of the		A GenomeMap in the ProMeTra context is a SVG based representation of the coding sequences (CDS) identified and annotated in the GenBank files of the
	individual prokaryotic database entries. GenomeMaps represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).		individual prokaryotic database entries. GenomeMaps represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).
	The order of the CDSs in the Grid representation is determined by basenumber of the stop codon counted from the origin of replication.		The order of the CDSs in the Grid representation is determined by the basenumber of the stop codon counted from the origin of replication.
	The grid is filled ~~rows first~~, i.e. the first ~~cds~~ is in ~~firts~~ row, first column, the second CDS is located at first row second column and so forth.		The grid is filled by row, i.e. the first CDS is in first row, first column, the second CDS is located at first row second column and so forth.
	A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates reverse strand.		A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates the location on the reverse strand.

	~~See~~ the following example of a GenomeMap for clarity:		Please see the following example of a GenomeMap for clarity:

	[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]		[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]

imported>HeikoNeuweger at 21:22, 9 March 2009

2009-03-09T21:22:13Z

← Older revision		Revision as of 23:22, 9 March 2009
Line 3:		Line 3:

	The replicons of prokaryotic genomes present in the NCBI genome database (as of Dez. 2008)		The replicons of prokaryotic genomes present in the NCBI genome database (as of Dez. 2008)
	have been converted into so called [[GenomeMaps]] for the [[ProMeTra]] web interface.		have been converted into so called GenomeMaps for the ProMeTra web interface.
	A [[GenomeMap]] in the [[ProMeTra]] context is a SVG based representation of the coding sequences (CDS) identified and annotated in the [[GenBank]] files of the		A GenomeMap in the ProMeTra context is a SVG based representation of the coding sequences (CDS) identified and annotated in the GenBank files of the
	individual prokaryotic database entries. [[GenomeMaps]] represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).		individual prokaryotic database entries. GenomeMaps represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).
	The order of the CDSs in the Grid representation is determined by basenumber of the stop codon counted from the origin of replication.		The order of the CDSs in the Grid representation is determined by basenumber of the stop codon counted from the origin of replication.
	The grid is filled rows first, i.e. the first cds is in firts row, first column, the second CDS is located at first row second column and so forth.		The grid is filled rows first, i.e. the first cds is in firts row, first column, the second CDS is located at first row second column and so forth.
	A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates reverse strand.		A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates reverse strand.

	See the following example of a [[GenomeMap]] for clarity:		See the following example of a GenomeMap for clarity:

	[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]		[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]

imported>HeikoNeuweger at 16:59, 4 March 2009

2009-03-04T16:59:19Z

← Older revision		Revision as of 18:59, 4 March 2009
Line 3:		Line 3:

	The replicons of prokaryotic genomes present in the NCBI genome database (as of Dez. 2008)		The replicons of prokaryotic genomes present in the NCBI genome database (as of Dez. 2008)
	have been converted into so called GenomeMaps for the [[ProMeTra]] web interface.		have been converted into so called [[GenomeMaps]] for the [[ProMeTra]] web interface.
	A GenomeMap in the ProMeTra context is a SVG based representation of the coding sequences (CDS) identified and annotated in the [[GenBank]] files of the		A [[GenomeMap]] in the [[ProMeTra]] context is a SVG based representation of the coding sequences (CDS) identified and annotated in the [[GenBank]] files of the
	individual prokaryotic database entries. [[GenomeMaps]] represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).		individual prokaryotic database entries. [[GenomeMaps]] represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).
	The order of the CDSs in the Grid representation is determined by ~~the base number~~ of the stop codon counted from the origin of replication.		The order of the CDSs in the Grid representation is determined by basenumber of the stop codon counted from the origin of replication.
	The grid is filled rows first, i.e. the first ~~CDS~~ is ~~loctated at first~~ row, first column, the second CDS is located at first row, second column and so forth.		The grid is filled rows first, i.e. the first cds is in firts row, first column, the second CDS is located at first row second column and so forth.
	A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates reverse strand.		A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates reverse strand.

	See the following example of a GenomeMap for clarity:		See the following example of a [[GenomeMap]] for clarity:

	[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]		[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]

	~~Each CDS is identified in the [[ProMeTra]] context by the ''locus_tag'' issued by the NCBI database.~~
	~~Datasets carrying these identifies can be mapped onto the genome maps.~~

imported>HeikoNeuweger at 16:57, 4 March 2009

2009-03-04T16:57:48Z

← Older revision		Revision as of 18:57, 4 March 2009
Line 3:		Line 3:

	The replicons of prokaryotic genomes present in the NCBI genome database (as of Dez. 2008)		The replicons of prokaryotic genomes present in the NCBI genome database (as of Dez. 2008)
	have been converted into so called [[GenomeMaps]] for the [[ProMeTra]] web interface.		have been converted into so called GenomeMaps for the [[ProMeTra]] web interface.
	A [[GenomeMap]] in the [[ProMeTra]] context is a SVG based representation of the coding sequences (CDS) identified and annotated in the [[GenBank]] files of the		A GenomeMap in the ProMeTra context is a SVG based representation of the coding sequences (CDS) identified and annotated in the [[GenBank]] files of the
	individual prokaryotic database entries. [[GenomeMaps]] represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).		individual prokaryotic database entries. [[GenomeMaps]] represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).
	The order of the CDSs in the Grid representation is determined by ~~basenumber~~ of the stop codon counted from the origin of replication.		The order of the CDSs in the Grid representation is determined by the base number of the stop codon counted from the origin of replication.
	The grid is filled rows first, i.e. the first ~~cds~~ is ~~in firts~~ row, first column, the second CDS is located at first row second column and so forth.		The grid is filled rows first, i.e. the first CDS is loctated at first row, first column, the second CDS is located at first row, second column and so forth.
	A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates reverse strand.		A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates reverse strand.

	See the following example of a [[GenomeMap]] for clarity:		See the following example of a GenomeMap for clarity:

	[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]		[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]

			Each CDS is identified in the [[ProMeTra]] context by the ''locus_tag'' issued by the NCBI database.
			Datasets carrying these identifies can be mapped onto the genome maps.

imported>HeikoNeuweger at 16:49, 4 March 2009

2009-03-04T16:49:56Z

New page

__NOTOC__
= [[GenomeMaps]] in [[ProMeTra]] =

The replicons of prokaryotic genomes present in the NCBI genome database (as of Dez. 2008)
have been converted into so called [[GenomeMaps]] for the [[ProMeTra]] web interface.
A [[GenomeMap]] in the [[ProMeTra]] context is a SVG based representation of the coding sequences (CDS) identified and annotated in the [[GenBank]] files of the
individual prokaryotic database entries. [[GenomeMaps]] represent CDS in a grid by individual rectangles labeled with the locus tag (or if available the gene name).
The order of the CDSs in the Grid representation is determined by basenumber of the stop codon counted from the origin of replication.
The grid is filled rows first, i.e. the first cds is in firts row, first column, the second CDS is located at first row second column and so forth.
A triangle at the right side of a rectangle indicates that the corresponding CDS is located on the forward strand, a triangle to the left indicates reverse strand.

See the following example of a [[GenomeMap]] for clarity:

[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]]