Hi Laura, You might find that Arabidopsis and rice (a monocot and a dicot) are too distant for this analysis, depending what you are trying to achieve. When I did a full genome scan of coding sequences, Arabidopsis and poplar (both dicots) are a bit too distant to get reasonable values - you tend to find a lot of genes where dS is saturated, so the dN/dS estimates are not very reliable. For an Arabidopsis/Papaya comparison, I found I could get decent values for around half the genome at least. If your objective is to get the values for the rice side of things, then maybe try maize as the comparator?
I'm afraid I can't help you with a public source for the data, I computed them myself using paml, but if you can't find what you need, drop me a line, and maybe there is something we can do together. Best wishes Dr. Jonathan Moore Senior Research Fellow in Bioinformatics -- Warwick Systems Biology Centre Coventry House University of Warwick Coventry CV4 7AL U.K. +44 (0)24 761 50332 http://go.warwick.ac.uk/jaymoore -----Original Message----- From: [email protected] on behalf of Arek Kasprzyk Sent: Mon 8/1/2011 1:52 PM To: Laura Roden Cc: [email protected] Subject: Re: [BioMart Users] synonymous vs non-synonymous coding: rice vsArabidopsis Hi Laura, i am assuming you are using Ensembl dataset. I am forwarding your email to the [email protected]. Someone from Ensembl will be able to help you a On Mon, Aug 1, 2011 at 6:23 AM, Laura Roden <[email protected]> wrote: > We are trying to compare orthologues in rice and Arabidopsis using BIoMart > and have selected the dS dN data, but the columns are returned blank. Is > this data available somewhere? > > All best wishes, > > Laura > > > Dr Laura Roden > Department of Molecular and Cell Biology > University of Cape Town > Private Bag Rondebosch > 7701 > Cape Town > South Africa > > http://www.mcb.uct.ac.za/Staff/Roden/lroden.htm > > ### > > UNIVERSITY OF CAPE TOWN > > This e-mail is subject to the UCT ICT policies and e-mail disclaimer > published on our website at > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 > 21 650 9111. This e-mail is intended only for the person(s) to whom it is > addressed. If the e-mail has reached you in error, please notify the author. > If you are not the intended recipient of the e-mail you may not use, > disclose, copy, redirect or print the content. If this e-mail is not related > to the business of UCT it is sent by the sender in the sender's individual > capacity. > > ### > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
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