[BiO BB] Re: characterization of an incomplete genome

Roy Chaudhuri roy at colibase.bham.ac.uk
Mon May 17 12:26:05 EDT 2004

>     We have assembled a Yesinia pestis genome. However, the genome is
> only 95% complete.  We would like to to characterize rearrangements,
> large, medium size indels,  repeat differences, gene differences by
> comparing it with a known complete genome.
>     I would appreciate if anybody could give me any advice or comments.

It is possible to compare unfinished genomes with related completed
genomes using BLAST and ACT (http://www.sanger.ac.uk/Software/ACT/), by
concatenating the contigs into a single sequence
(see: http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00107.html
for a fuller description.)

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


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