ProMeTraWiki/GenomeMaps: Difference between revisions
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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 | have been converted into so called GenomeMaps for the [[ProMeTra]] web interface. | ||
A | 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 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 | 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 | 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. | |||
Revision as of 17:57, 4 March 2009
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 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 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.
See the following example of a GenomeMap for clarity:
File: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.