CMR Searches

Gene Searches

• Annotation Search: Search for a string in the annotation of a genome. This includes searches of the loci names, gene symbols, and common names of the genomes selected. The tool will return to you a list of all genes that contain the search string.


• SWISS-PROT/TrEMBL Search: Get a list of all genes assigned a specific SWISS-PROT or TrEMBL number.


• GenBank Search: Get a list of all genes assigned a specific GenBank number.


• EcoCyc Search: Get a list of genes assigned a specific EcoCyc number.


• EC Number Search: Get a list of genes assigned a specific Enzyme Commission number.


• Gene Ontology Search: Get a list of all genes assigned a specific Gene Ontology (GO) term.


• TIGRFAM/Pfam Search: Get a list of all genes that hit a specific HMM, either TIGRFAM or Pfam.


• COG Search: Get a list of all genes that hit a specific NCBI Clusters of Orthologous Groups of proteins (COG) number.


• Interpro Search: Get a list of all genes that hit a specific Interpro accession number.


• PROSITE Search: Get a list of all genes that hit a specific PROSITE accession number.


• TIGR Role Category Search: Get a list of all genes assigned the selected TIGR role category/categories.


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

Genome Searches

• Genome Text Search: Get a list of all Genomes whose organism name or sequencing center match a text string.


• Genome Property Search: Get a list of genomes and their properties.

Sequence Searches

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


• TIGRFAM/Pfam Sequence Search: Search a sequence against protein family based HMMs.


• 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.


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

Evidence/Text Searches

• Text Search: Get a list of all TIGRFAM, Pfam, EC, GO, Interpro, PROSITE, and COG terms that match a text string.


• EC Term Text Search: Get a list of all EC terms that match a text string.


• GO Term Text Search: Get a list of all GO Terms that match a text string.


• TIGRFAM/Pfam Text Search: Get a list of all HMMs, either TIGRFAM or Pfam, that match a text string.


• COG Text Search: Get a list of all COGs that match a text string.


• Interpro Text Search: Get a list of all Interpros that match a text string.


• PROSITE Text Search: Get a list of all PROSITEs that match a text string.


• Genome Properties search: Displays Genome Properties that match a given text string


• EGAD search: Displays EGAD description for a given EGAD number


• CMR Tools Search: Get a list of all tools matching a given text string.