[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.)
Roy.
--
Dr. Roy Chaudhuri
Bioinformatics Research Fellow,
Division of Immunity and Infection,
University of Birmingham, UK
http://colibase.bham.ac.uk
More information about the BBB
mailing list