Comparative Tools

The NMPDR offers a set of genome caparison tools for analyzing the genomic data in our database.

Annnotation Clearinghouse

The Annotation Clearinghouse contains annotations from all the major databases as well as assertions submitted by experts. Selecting a genome in this tool will show you all the clearinghouse annotations for that genome.

Homolog Spreadsheet

The Homolog Spreadsheet Tool compares all proteins in the selected genomes to those in a reference genome. The results are presented in a table, with different genomes shown side-by-side in columns, and proteins in rows. The proteins are listed in order of their appearance in the selected reference genome.

Signature Genes Tool

The motivation for the Signature Genes Tool is to try to locate genes related to a phenotype that is associated with one set of organisms (call this set1) but not with another (call these set2).

The search goes through the genes in one organism from Set 1, selected as the reference genome. For each gene in the reference genome, the tool evaluates the bidirectional best hits of the genes that occur in genomes from set1 and set2. It tabulates these and constructs a score from 0 to 1. A score of 1 means that the gene has a bidirectional best hit in every genome from set1 and no bidirectional best hits against any genome in set2.

The scores are tabulated. The best candidate genes are then presented to you as a list of genes to explore. The main shortcoming of the tool relates to our use of bidirectional best hits. If there are paralogs to the gene within genomes, a bidirectional best hit may not exist in a genome that contains several clear homologs. This means that we may miss genes with paralogs, and we may include genes that do not discriminate as well as we seem to indicate. This means that you must explore each gene as a candidate, but nothing more. There is now the option of running the tool using precomputed similarities rather than bidirectional best hits.

Topic revision: r4 - 15 Feb 2009 - 17:10:06 - TWiki Guest
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (, a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.