Re: [BioMart Users] synonymous vs non-synonymous coding: rice vs Arabidopsis

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] synonymous vs non-synonymous coding: rice vs Arabidopsis

Arek Kasprzyk
Hi Laura,
i am assuming you are using Ensembl dataset. I am forwarding your
email to the [hidden email]. Someone from Ensembl will be able to
help you

a

On Mon, Aug 1, 2011 at 6:23 AM, Laura Roden <[hidden email]> 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
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] synonymous vs non-synonymous coding: rice vs Arabidopsis

whsqwghlm
Hi Laura,

This would be a Gramene/Ensembl Genomes dataset. We've never been able to get the dN/dS data to build correctly from the Ensembl Compara GeneTree pipeline, either at EBI or CSHL. So sorry - this data is not available anywhere.

Best,

Will

On 1 Aug 2011, at 13:52, Arek Kasprzyk wrote:

> Hi Laura,
> i am assuming you are using Ensembl dataset. I am forwarding your
> email to the [hidden email]. Someone from Ensembl will be able to
> help you
>
> a
>
> On Mon, Aug 1, 2011 at 6:23 AM, Laura Roden <[hidden email]> 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
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users

--
William Spooner
[hidden email]
http://www.eaglegenomics.com



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] synonymous vs non-synonymous coding: rice vs Arabidopsis

Laura Roden
Thanks very much!
 
All best wishes,
laura

>>> William Spooner <[hidden email]> 2011/08/01 03:15 PM >>>
Hi Laura,

This would be a Gramene/Ensembl Genomes dataset. We've never been able to get the dN/dS data to build correctly from the Ensembl Compara GeneTree pipeline, either at EBI or CSHL. So sorry - this data is not available anywhere.

Best,

Will

On 1 Aug 2011, at 13:52, Arek Kasprzyk wrote:

> Hi Laura,
> i am assuming you are using Ensembl dataset. I am forwarding your
> email to the [hidden email]. Someone from Ensembl will be able to
> help you
>
> a
>
> On Mon, Aug 1, 2011 at 6:23 AM, Laura Roden <[hidden email]> 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
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users

--
William Spooner
[hidden email]
http://www.eaglegenomics.com




###

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
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: [BioMart Users] synonymous vs non-synonymous coding: rice vsArabidopsis

jonathan.moore@warwick.ac.uk
In reply to this post by Arek Kasprzyk
RE: [BioMart Users] synonymous vs non-synonymous coding: rice vsArabidopsis

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: [hidden email] on behalf of Arek Kasprzyk
Sent: Mon 8/1/2011 1:52 PM
To: Laura Roden
Cc: [hidden email]
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 [hidden email]. Someone from Ensembl will be able to
help you

a

On Mon, Aug 1, 2011 at 6:23 AM, Laura Roden <[hidden email]> 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
[hidden email]
https://lists.biomart.org/mailman/listinfo/users


_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users