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