GeneCensus Browser

This page provides data on the comparative analysis of 8 genomes (listed below) in terms of protein structures. It is part of an overall effort on large-scale, structural censuses of the sequence databanks and functions as supplementary material to the following paper (and other papers currently under review).

Gerstein (1997). "A Structural Census of Genomes: Comparing Eukaryotic, Bacterial and Archaeal Genomes in terms of Protein Structure," J. Mol. Biol. 274, 562-576.

1. Detailed Analysis of the Fold Usage

Many formatted text tables giving statistics on fold usage
Top-10 fold in the genomes [gif, pdf, help]
The Detailed Fold Usage for Each Fold in Each Genome
[html, html-big, pdf, DB-text-table, DB-table-header, help]
Condensed Summary of Fold Usage Patterns in terms of Binary Numbers
Graphs of Frequency of TM-helices [Normal, log-log]
Search for the Number of Times a Fold Corresponding to a PDB ID Occurs in Various Genomes:

2. Tables comparing genomes and PDB in terms of simple statistics

Many formatted text tables with statistics on length, composition, and membrane proteins.
Composition Comparison [excel-file]

3. Specific analysis tables for each genome and the PDB

Click on an abbreviation name for a list of local tables pertinent to each genome. These tables make extensive use of the idea of "masking" various regions of the genome. (Help on this idea.)

Abbrev.	Genome	Size (Mb)	Reference	Website URL (http://…)
HI	Haemophilus influenzae	1.83	Fleischmann et. al., Science 269:496-512 (1995)	www.tigr.org/tdb/mdb/hidb/hidb.html
MG	Mycoplasma genitalium	0.58	Fraser et. al., Science 270:397-403 (1995)	www.tigr.org/tdb/mdb/mgdb/mgdb.html
MJ	Methanococcus jannaschii	1.66	Bult et. al., Science 273:1058-1073 (1996)	www.tigr.org/tdb/mdb/mjdb/mjdb.html
SS	Synechocystis sp.	3.57	Kaneko et. al., DNA Res. 3: 109-136 (1996)	www.kazusa.or.jp/cyano/cyano.html
MP	Mycoplasma pneumoniae	0.81	Himmelreich et. al., Nuc. Acid Res. 24:4420-4449 (1996)	www.zmbh.uni-heidelberg.de/ M_pneumoniae/MP_Home.html
SC	Saccharomyces cerevisiae	13	Goffeau et. al., Nature 387 (Suppl.) 5-105 (1997)	genome-www.stanford.edu/ Saccharomyces
HP	Helicobacter pylori	1.66	Tomb et. al., Nature 388:539-547 (1997)	www.tigr.org/tdb/mdb/hpdb/hpdb.html
EC	Escherichia coli	4.60	Blattner et. al., Science 277:1453-1462 (1997)	www.genetics.wisc.edu
PS	Soluble PDB (for comparison)		Abola et al. Meth. Enz. 277: 556-571 (1997).	www.pdb.bnl.gov
TP	Treponema pallidum	1.14	-	utmmg.med.uth.tmc.edu/treponema/tpall.html

4. Help and Information Document

This gives the specific methods used for the calculations.

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