identify syntenic position in Drosophila

[Piero]

Hello

I am interested in looking at syntenic conservation of regions of non-coding DNA in a few Drosophila species. 

I read a few post in here and have the following questions:

Do you think I could use the netFilter -syn script with a distant pair of species such as dm3/drovir3? The guidelines suggest that this be used only for closely related species, however I was wondering if you believe that it could be fine in my case. Also I read in a post that the tool is optimized for human and hg closely related species. Do you have any suggestion on how to change parameters for use in Drosophila?

If you think the above strategy won't be effective in identifying syntenic positions, do you have any suggestion on the best tool or strategy to pool out all syntenic regions from pairwise allignments between two Drosophila species?

Thanks a lot for you help and your great work on the UCSC Genome Browser

Piero

PhD candidate - MSKCC/GSK

[Matthew Speir]

Hi Piero,

Thank you for your question about identifying syntenic positions in
Drosophila.

Unfortunately, I'm not sure that we can predict how well that method
would work in this case.

However, you are more than welcome to try this netFilter -syn method
with a few different parameter sets and see what the results are and if
they seem reasonable. You can look at the resulting alignments in a few
different regions in the Genome Browser to evaluate whether the results
will suit your needs.

You may also want to ask your question on a more general biology forum
such as Biostars, https://www.biostars.org/.

I hope this is helpful. If you have any further questions, please reply
to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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