[Inparanoid] DNA?
Ivo Rieu
I.Rieu at science.ru.nl
Fri Jul 15 22:31:44 CEST 2011
Dear Inparanoid,
My question is whether InParanoid can also work on DNA. I work with two
closely related plant species (Solanum lycopersicum and Solanum
dulcamara). While the tomato genome has been sequenced at high standard by
a consortium, we have assembled the transcriptome of S. dulcamara
ourselves from several Illumia HiSeq lanes. I am not sure whether it would
be wise to look for orthologs between the two species using translations,
because mistakes in our assembled contigs would mess up the search.
Because the species are closely related (orthologs are >90% identical in
de CDS), I was wondering whether Inparanoid would work on DNA. If not,
would you know another program or another strategy?
Thank you in advance.
Sincerely,
Ivo Rieu
_____________________________
Dr. Ivo Rieu
Assistant Professor
Department of Molecular Plant Physiology
Institute for Water and Wetland Research
Faculty of Science
Radboud University
Postbus 9010
6500 GL Nijmegen
The Netherlands
Visiting address:
Huygens building, room HG 02.307
Heyendaalseweg 135, 6525 AJ Nijmegen
Contact:
TEL +31 (0)24 3652761
FAX +31 (0)24 3652490
EMAIL i.rieu at science.ru.nl
WEB http://www.ru.nl/mpp/
More information about the InParanoid
mailing list