Hi Mungo,
This was EXACTLY what I needed. Thank you very much!
As my alignment is huge, writing to Groovy output didn't work well. But saving
to a file solved the problem.
Best regards,
Romain
Sent with [ProtonMail](https://protonmail.com) Secure Email.
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Tuesday, November 27, 2018 1:33 PM, Mungo Carstairs (Staff)
<g.m.carsta...@dundee.ac.uk> 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
>
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> 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
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> ---------------------------------------------------------------
>
> From: jalview-discuss-boun...@jalview.org
> <jalview-discuss-boun...@jalview.org> on behalf of Romain Studer
> <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
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