A Functional Map of the Proteome

LGL: Creating a map of protein function with an algorithm for visualizing very large biological networks

Alex Adai, Shailesh V. Date, Shannon McDonald and Edward M. Marcotte

Supporting materials for the paper submitted to Journal of Molecular Biology :

List of the 50 genomes used in the analysis.

List of the ~145,000 genes used in the analysis.
Each line refers to a single gene, for example:
>afulgidus|gi|11497622|ref|NP_068842.1| A. fulgidus predicted coding region AF0001 [Archaeoglobus fulgidus]
Here, 'afulgidus' refers to the organism (Archaeglobulus fulgidus) and the number following the code 'gi' (11497622) is the identification number in Genbank, where more information can be found about each gene and its sequence.

Raw data for the protein homology graph

The graph constructed with BLAST threshold of log E < -12

The largest connected set - The edge file contains the complete set of sequence similarity edges in the protein homology graph. Each vertex id in this file is the Genbank gi code, which can be either matched to protein names from the gene name file listed above or from Genbank. In some cases a gi code is not available for a protein, so instead an 'x' + Integer is used. The Integer used represents the order of occurance of that protein in the above gene list.
2D Coordinates - The coordinates of each protein corresponding to the above edge file.

Data for all connected sets: .lgl file | .coords file

The LGL suite of programs, and documentation on usage including source code are available through the LGL page. Note than on a 2.8GHz PC with 2GB RAM running WindowsXP, the viewer takes several minutes to load the graph, and can be VERY slow to navigate. We have noticed better performance on Linux boxes for the viewer.

Mail comments/questions to Edward Marcotte at marcotte@icmb.utexas.edu.

Last modified: December 1, 2003

Copyright © 2002, 2003 Alex Adai, Shailesh Date, Shannon McDonald, and Edward Marcotte. This site is not intended for commercial use. The protein homology graph data and server is the property of the Regents of the University of Texas, and cannot be used for commercial purposes without written permission of Edward Marcotte and the Regents of UT. It is forbidden to redistribute, derivatize, or encapsulate the protein homology graph server or data in another database without permission. Sale of information derived from it, whether directly or in revised form, is forbidden except by permission of UT and Edward Marcotte. All copies or mirrors of the protein homoloy graph server must carry this notice.