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Homolog Spreadsheet Tool

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. This tool is in development in the SEED environment. As an example, see the results of a comparison of Campylobacter jejuni jejuni genomes.

After selecting a set of genomes to compare from the list below and clicking the button, you will be directed to a page where you can choose the reference genome and the column order of the comparison genomes. The result may take a while to calculate, especially if you selected a large group of genomes. The results table is color-coded to reflect the similarity of the protein sequences, from Violet (100%), through visual spectrum to Red.

  Percent protein sequence identity
Bidirectional best hit 100 99.9 99.8 99.5 99 98 95 90 80 70 60 50 40 30 20 10
Unidirectional best hit 100 99.9 99.8 99.5 99 98 95 90 80 70 60 50 40 30 20 10

Input Form


  

Optionally, to focus the comparison on a region of the genome, enter the FigId of the gene of interest and the size of the region to be compared
Fig ID
Region Size
Topic revision: r11 - 18 Aug 2008 - 21:33:36 - RobertOlson
Main.HomologSpreadsheet moved from Main.CompareGenomes on 19 Mar 2008 - 22:35 by BruceParrello - put it back
 
NMPDR is 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.