Jena Prokaryotic Genome Viewer

The Jena Prokaryotic Genome Viewer (JPGV) is a freely accessible web tool aimed at visualization and analysis of prokaryotic genomes.

JPGV currently includes 1140 genomic elements of 293 species.

You can use JPGV to ...
Generate circular plots displaying genome features of one ore more complete genomes [ PDF: Example 1 \| Example 2 ] Generate linear plots displaying genome features of a genome part or of a complete genome [ PDF: Example, coloring according to GOG functional categories ] (In addition to features included in the GenBank file values of GC content, GC skew, purine excess and keto excess can be displayed) Generate circular or linear genome plots by filtering the complete gene set with information from external databases or from COG functional categories Generate clickable linear whole genome views displaying genes coloured according to their COG functional classification Generate genome lists with gene numbers, genome lengths, average GC-content and fraction of hypothetical and putative genes Do a QuickSearch across all genomes Select genes of all genomes for a specific COG functional category Select all genes of a certain species for which entries in one of more than 60 databases cross-referenced by UniProt are available (Advanced search) Examples: Generate a list of all genes from Helicobacter pylori for which three-dimensional structures of the protein are known Generate a gene list for another species for which Pfam or Smart information is available Select gene lists for one or all genomes according to such gene features as GC-content and length Search for sequence motifs in one or all genomes adopting the pattern syntax used in the PROSITE database Store search results in lists and to use them for generating plots (This requires online registration) Do a BLAST search for gene/protein or your own sequences within the JPGV database or UniProt Display gene information in a compact manner on the gene information sheet Display predicted horizontally transferred genes as table and as clickable whole genome view Generate lists of best bidirectional hits between the proteins of two genomes by using OMA data Display lists of all related genes of two or more genomes or genomic elements (Gene core sets) Analyse syntenies between different genomes based on the best bidirectional hits Display the codon and amino acid usages of one or more genomes or genomic elements Perform a statistical analysis of sequence differences
More information on these options can be found in the documentation.

You can use JPGV to ...

Generate circular plots displaying genome features of one ore more complete genomes [ PDF: Example 1 | Example 2 ]
Generate linear plots displaying genome features of a genome part or of a complete genome [ PDF: Example, coloring according to GOG functional categories ]
(In addition to features included in the GenBank file values of GC content, GC skew, purine excess and keto excess can be displayed)
Generate circular or linear genome plots by filtering the complete gene set with information from external databases or from COG functional categories
Generate clickable linear whole genome views displaying genes coloured according to their COG functional classification
Generate genome lists with gene numbers, genome lengths, average GC-content and fraction of hypothetical and putative genes
Do a QuickSearch across all genomes
Select genes of all genomes for a specific COG functional category
Select all genes of a certain species for which entries in one of more than 60 databases cross-referenced by UniProt are available (Advanced search)
Examples:
Generate a list of all genes from Helicobacter pylori for which three-dimensional structures of the protein are known
Generate a gene list for another species for which Pfam or Smart information is available
Select gene lists for one or all genomes according to such gene features as GC-content and length
Search for sequence motifs in one or all genomes adopting the pattern syntax used in the PROSITE database
Store search results in lists and to use them for generating plots
(This requires online registration)
Do a BLAST search for gene/protein or your own sequences within the JPGV database or UniProt
Display gene information in a compact manner on the gene information sheet
Display predicted horizontally transferred genes as table and as clickable whole genome view
Generate lists of best bidirectional hits between the proteins of two genomes by using OMA data
Display lists of all related genes of two or more genomes or genomic elements (Gene core sets)
Analyse syntenies between different genomes based on the best bidirectional hits
Display the codon and amino acid usages of one or more genomes or genomic elements
Perform a statistical analysis of sequence differences

More information on these options can be found in the documentation.