CMR Genomes

Lists

• All CMR Genomes ordered by organism name: This tool lists all organisms in the CMR ordered alphabetically. It also includes additional information on the genomes and useful links.


• All CMR Genomes ordered by taxonomy: This tool lists all CMR organisms in a taxonomic tree that can be expanded or collapsed.

Summary Information

• Genome Properties: Provides information on the characteristics of organisms derived from genomic data and literature sources.


• DNA Molecule Information: This tool provides detailed information on each of the DNA molecules found in the organism (chromosomes, plasmids) including the topology (linear or circular), length, %A, T, G, C and number of genes.


• All Genes in a Genome: Lists all genes in the selected genomes.


• Role Category Pie Chart: Shows the number and percentage of genes in a selected genome for every role category in the CMR.


• Role Category Bar Chart: Shows the number and percentage of genes in the CMR assigned to each of the role categories.


• Terminator Bar Chart: Shows the number and percentage of genes in each genome predicted to have Rho-independent terminators.


• Intergenic Regions: Lists all the intergenic regions for a selected DNA molecule.


• InterRNA Regions: Lists all the interRNA regions for a selected DNA molecule.

Graphical Displays

• Compact Genome Display: Shows all of the genes on a DNA molecule as different colored stars in a linear graphic. The colors represent different functional roles.


• Circular Genome Display: Shows a circular image of a selected DNA molecule. The image includes representation of all genes on the molecule as well as all tRNAs and rRNAs.


• Display Region of Genome: View a graphical display of a small region of DNA either between a pair of coordinates or surrounding a particular gene. The display shows the location, direction and reading frame of genes in that region.

Analysis Tools

• Position Search/Segment Retrieval: Retrieve sequence or a list of genes between a pair of coordinates for the selected DNA molecule.


• Third Position GC Skew Display: Predicts genes by comparing possible open reading frames to a third position GC plot.


• Restriction Digest: Displays restriction digest information for a genome.


• Pseudo 2D Gel: Shows a computer model of a 2-Dimensional gel for a selected organism.


• Putative Operon Predictions: Use this page to view TIGR's predictions of putative operons in microbial genomes.


• GC Content Display: Shows the %GC for a set "window" of nucleotides across the entire DNA molecule. The user has the option to change the size of the %GC window.


• Codon Usage: Shows codon usage within a genome. The user may limit included sequences by role category, molecule, and coordinates.


• Protein Motif Search: Search all proteins in a genome for a given motif


• CMR BLAST: Search based on a sequence (nucleotide or peptide).