ProMeTraWiki/GenomeMaps: Difference between revisions
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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 | 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. | ||
Please see the following example of a GenomeMap for clarity: | |||
[[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]] | [[Image:ProMeTraWiki$$GenomeMaps$genomemap.png]] | ||
Revision as of 15:04, 13 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 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:
