[BiO BB] RE: E.coli strain differences (Chandran Vijayendran)

[William Hsiao]

I think you can use MUMmer (http://www.tigr.org/software/mummer/) to
align the two genomes and extract regions in W3110 that do not align
with MG-1655.  Since MUMmer (specifically NUCmer) produces a linear
alignment, gene rearrangements show up as alignments off the x=y
diagonal and additional genes show up as gaps.  You can extract
sequences from off-centered alignments and gaps, and perform BLAST
analysis to find out the gene content (or if the genomes are annotated,
read them off an annotation file such as .ptt files from NCBI).

Cheers

Will

William Hsiao
PhD Student, Brinkman Laboratory
Department of Molecular Biology and Biochemistry
Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada V5A 1S6
Phone: 604-291-4206 Fax: 604-291-5583
 

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Today's Topics:

   1. E.coli strain differences (Chandran Vijayendran)

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Message: 1
From: "Chandran Vijayendran" <vijayendran_vijay at hotmail.com>
To: bio_bulletin_board at bioinformatics.org
Date: Wed, 05 May 2004 10:48:00 +0000
Subject: [BiO BB] E.coli strain differences
Reply-To: bio_bulletin_board at bioinformatics.org


Dear all,

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 
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?

Thanks for your time,

-Vijay-

öööööööööööööööööööööööööööööööööööööööööö
Chandran Vijayendran,
PhD Student,
Graduate school in Bioinformatics and Genome research.
c/o Prof. Erwin Flaschel,D5-120. Technical faculty,
University of Bielefeld,Universitaets str -25,D-33615,Bielefeld.
Germany.

Phone
Home: + 49 (0)521-3279769.
Off: + 49 (0)521-1065286.
Mobile: + 49 (0)17624024791.
öööööööööööööööööööööööööööööööööööööööööö

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