[Computational-biology] Re: Help with a bioinformatics problem

Kevin Karplus karplus at cheep.cse.ucsc.edu
Sun Aug 7 16:43:16 EST 2005

On 2005-08-05, Thomas Jahns <Thomas.Jahns at epost.de> wrote:
> "JoeT" <trubisz at yahoo.com> writes:
>> i'm trying to do a genome (i think) comparison between A. agrarius, R
>> novegius, C glareolus and being new to bioinformatics, i'm not exactly
>> sure what would be the best nucleotide or genome part that i should
>> select is doing a multiple sequence analysis.
>> can someone point me to the correct thing i should do?
> You should perhaps describe in more detail what you intend to
> compare. While the chromosomes of a genome may be available as single
> sequences, it's usually only single genes which are subjected to
> multiple alignment.

Not quite true.  There are alignments of whole genomes done for
finding syntenic blocks.  These can be particularly useful when
looking for operons in bacterial genomes.  For computational reasons,
they are done as pairwise alignments, but they are sometimes
interpreted as multiple alignments.

Doing synteny mapping for large genomes is a bit tricky, as it is easy
to be mislead by repeats.  The UCSC genome browser group has done
several whole-genome alignments, including rat, mouse, human, chicken,
... , but not A. agrarius or C. glareolus.  http://genome.ucsc.edu/

Their tools are available---you probably want to use BLAT, by Jim
Kent, though there may be other relevant tools.

Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors, ISCB)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
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