Hi Mungo,
Yes, I needed the scores against the consensus, which was provided by your
script.
I was already able to extract the conservation score from Jalview.
Many thanks for your help,
Romain
Sent with [ProtonMail](https://protonmail.com) Secure Email.
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Wednesday, November 28, 2018 8:59 AM, Mungo Carstairs (Staff)
<g.m.carsta...@dundee.ac.uk> wrote:
> To avoid confusion(?)
>
> - my script generates Blosum62 scores against consensus, not conservation
> score
>
> - conservation scores can be output from Jalview using [Export
> Annotation](http://www.jalview.org/help/html/menus/alwannotationpanel.html)
>
> Romain, you might want to make a slight adjustment to the script to calculate
> an average score, rather than a total, if there is a 'joint consensus' (tie).
>
> Example:
>
> Residue L, consensus M, Blosum62 score = 2
>
> Residue L, consensus I, score = 2
>
> Residue L, joint consensus [IM], score = 2 + 2 = 4 // a score of 2 would make
> more sense
>
> It makes no difference to the colour scheme, as it only cares if the score is
> positive or not, but an average would be more 'correct' for other analysis.
>
> Just add one line:
>
> score /= consRes.length();
> print(score);
>
> Mungo
>
> [University of Dundee shield logo](http://uod.ac.uk/sig-home)
>
> Mungo Carstairs
> Jalview Computational Scientist
>
> The Barton Group
> Division of Computational Biology
>
> School of Life Sciences
>
> University of Dundee, Dundee, Scotland, UK
>
> www.jalview.org
>
> www.compbio.dundee.ac.uk
> g.m.carsta...@dundee.ac.uk
>
> [University of Dundee Facebook](http://uod.ac.uk/sig-fb) [University of
> Dundee Twitter](http://uod.ac.uk/sig-tw) [University of Dundee
> LinkedIn](http://uod.ac.uk/sig-li) [University of Dundee
> YouTube](http://uod.ac.uk/sig-yt) [University of Dundee
> Instagram](http://uod.ac.uk/sig-ig) [University of Dundee
> Snapchat](http://uod.ac.uk/sig-sc)
>
> [We're Scottish University of the Year again!](http://uod.ac.uk/sig-strapline)
> The Times / Sunday Times Good University Guide 2016 and 2017
> ---------------------------------------------------------------
>
> From: Geoffrey Barton (Staff)
> Sent: 27 November 2018 23:32:03
> To: Mungo Carstairs (Staff); jalview-discuss@jalview.org; Romain Studer
> Subject: Re: [Jalview-discuss] Retrieve score for conservation at the
> individual amino acid level
>
> Hi Romain,
>
> If it is just the conservation score you are interested in, then other
> software can give this to you too. You can get this by uploading your
> alignment to the AMAS server or running AMAS locally, alternatively ALSCRIPT
> also has a function to generate the conservation score.
>
> Still, Mungo's solution does it nicely in Jalview, so probably best to stick
> with that!
>
> Geoff.
>
> On 27/11/2018 13:33, Mungo Carstairs (Staff) wrote:
>
>> Hi Romain,
>>
>> Try running the attached script in the Jalview Groovy console - it should
>> output residue Blosum62 scores against the alignment consensus.
>>
>> Regards,
>>
>> Mungo
>>
>> Email signature
>>
>> [University of Dundee shield logo](http://uod.ac.uk/sig-home)
>>
>> Mungo Carstairs
>> Jalview Computational Scientist
>>
>> The Barton Group
>> Division of Computational Biology
>>
>> School of Life Sciences
>>
>> University of Dundee, Dundee, Scotland, UK
>>
>> www.jalview.org
>>
>> www.compbio.dundee.ac.uk
>> g.m.carsta...@dundee.ac.uk
>>
>> [University of
>> Dundee Facebook](http://uod.ac.uk/sig-fb) [University of
>> Dundee Twitter](http://uod.ac.uk/sig-tw) [University of
>> Dundee LinkedIn](http://uod.ac.uk/sig-li) [University of
>> Dundee YouTube](http://uod.ac.uk/sig-yt) [University of
>> Dundee Instagram](http://uod.ac.uk/sig-ig) [University of
>> Dundee Snapchat](http://uod.ac.uk/sig-sc)
>>
>> [We're Scottish University of the Year
>> again!](http://uod.ac.uk/sig-strapline)
>> The Times / Sunday Times Good University Guide 2016 and 2017
>>
>> ---------------------------------------------------------------
>>
>> From: jalview-discuss-boun...@jalview.org
>> [<jalview-discuss-boun...@jalview.org>](mailto:jalview-discuss-boun...@jalview.org)
>> on behalf of Romain Studer
>> [<evosit...@protonmail.com>](mailto:evosit...@protonmail.com)
>> Sent: 27 November 2018 11:35:24
>> To: jalview-discuss@jalview.org
>> Subject: [Jalview-discuss] Retrieve score for conservation at the individual
>> amino acid level
>>
>> Hi,
>>
>> I am wondering if we can extract the score to do the colour map from an
>> alignment?
>>
>> For example, if we colour the alignment with Blosum62 (for example) and we
>> select Colour by conservation, with a threshold of 30,
>> we will get column that are white, and some columns with various level of
>> blue/purple.
>> And some outlier AA in those column will be kept still white or less bright.
>> I guess this is based from the AMAS method?
>>
>> Can we retrieve this information directly from Jalview and output the scores
>> as a 2d matrix (genes x positions)?
>> Or is there a tool to compute such conservation score at the individual
>> amino acid level?
>>
>> Thanks,
>> Romain
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>> _______________________________________________
>> Jalview-discuss mailing list
>> Jalview-discuss@jalview.org
>>
>> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
>
> --
> Geoff Barton | Professor of Bioinformatics | Head of Division of
> Computational Biology
> School of Life Sciences | University of Dundee, Scotland, UK |
> g.j.bar...@dundee.ac.uk
> Tel: +44 1382 385860 |
> www.compbio.dundee.ac.uk
> | twitter: @gjbarton
>
> The University of Dundee is registered Scottish charity: No.SC015096
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
