[BiO BB] RE: E.coli strain differences

[Roy Chaudhuri]

> I would like to compare the whole genome of two E.coli strains, 
> (K12-MG-1655 and K12 W3110). Where MG strain genome is available at
> NCBI and W3110 strain genome is=20 available at Genobase. I would
> like to know gene arrangement differences in both the strain. Is this
> data is already available on net? If not how shall I proceed on?

Our database coliBASE (http://colibase.bham.ac.uk) is a comparative
genomics database for analysis of E.coli and its relatives. It includes
precalculated MUMmer (and PROmer) alignments and has a built in
user-friendly online display tool, to save you the bother of downloading
ACT. The database includes K12 MG1655 and W3110, as well many other genomes.

This link:
http://colibase.bham.ac.uk/cgi-bin/viewgenome.cgi?accession=U00096&scheme=ortho&frame=genome&help=genomechoose&palette=gr&genome=ECO_W3110

shows a whole genome view of K12 MG1655, with the genes coloured in
according to the presence or absence of orthologues in W3110 (genes with
no annotated orthologue are coloured in red). From this global view it's
easy to identify regions of difference, and these can be viewed in
detail by clicking on them.

For example:
http://colibase.bham.ac.uk/cgi-bin/contigalignment.cgi?accession=U00096&start=2549822&end=2569821&display=arrow&scale=33&alnacc=ECO_W3110

this link shows one of the (very few) regions of difference between the
two strains, with an insertion in MG1655 that is absent from W3110,
highlighted using MUMmer.

A description of coliBASE was published in the NAR database issue which
is freely available on the web:
http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D296

Oh, and sorry for the blatant advertising, but if anyone's interested we
have similar databases for Pseudomonas (http://pseudo.bham.ac.uk),
Campylobacter and related genera (http://campy.bham.ac.uk) and
Clostridium (http://clostri.bham.ac.uk).

Roy.
--
Dr. Roy Chaudhuri
Bioinformatics Research Fellow,
Division of Immunity and Infection,
University of Birmingham, UK

http://colibase.bham.ac.uk