Hello,

I have been trying to analyse the DNA sequence of a myosin gene in Drosophila melanogaster that is well conserved among the other Drosophila species (the 20 that are sequenced). We know it is responsible for a phenotype that, however is not conserved but follows a phylogenetic pattern. This phenotype is conserved in a subgenus but not in the other 2 subgenus. So we are trying to match the specific DNA sequences which changes are responsible for this variation. However, the protein sequence is 97% identical and there is no aminoacid change that comprises one subgenus and not the other. Also, this phenotype is tissue specific and another tissue specific phenotype is conserved among all the species and probably among all insect orders.Therefore, we think it might not be the coding sequence the responsible for such tissue specific variation.

Lately we have been trying to implement the "Detecting Selection in Noncoding Regions of Nucleotide Sequences" method to analyse the noncoding part of the gene.(Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login) from Neilsen group. So, I was wondering if you already have experience with such analysis and can it be done in the datamonkey server?

Thanks for the help,
Nica

PS: I didnt write any specific information regarding the gene or the phenotype to avoid confusion, but I am quite happy to discuss this information if asked 

Hi,

Thanks for the fast response I will check the other posts and try to use the batch file you uploaded there.

Nica