[Inparanoid] DNA?

[Ivo Rieu]

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

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