* 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

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

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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