Hi Aaron,
I am trying to use Mauve for aligning human exome sequences. I
know this is not the conventional use of Mauve, but I think it shouldn't
be too hard to get done. Each of the exomes consists of ~30,000
genes/contigs and the total size of the contigs is ~30MB. I have been
able to get Mauve to just do a simple alignment of the contigs, but that
is not very useful for me. My main purpose in doing the comparative
alignment of the two exomes is to identify rearrangements between them.
In order to effectively do this, I need to be able to do one of two
things, but preferably both of them.
1. Have Mauve maintain the names of my contigs so that I can look at the
alignment and see which contigs from one exome align to two contigs of
the other exome (indicating a rearrangment). The exomes are in fsta
format with the contig names in the tags.
2. Align the exomes to the set of Human Genes from Genbank. I have
tried downloading the full set of human genes from Genbank, but Mauve
will not accept it.
Thank you for your help,
Jeff
--
Jeffrey Rosenfeld Ph. D.
Research Scientist
Laboratory of Analytic Genomics, Division of Psychiatry Research,
The Zucker Hillside Hospital;
North Shore - Long Island Jewish Health System;
Mailing Address:
The Zucker Hillside Hospital
Psychiatry Research
75-59 263rd Street
Glen Oaks, NY 11004
718-470-8836 (ph)
718-343-1659 (fax)
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