Hi Romain,
I'm not quite sure if you want conservation scores, or BLOSUM scores, or both... 'Colour by Conservation' uses conservation score to 'fade' whatever colour scheme is selected. http://www.jalview.org/help/html/colourSchemes/conservation.html The conservation score is per column of the alignment, not per residue. You can get it by right-clicking on the Conservation annotation label, and 'Export Annotation'. Jalview's Blosum62 colour scheme is described at http://www.jalview.org/help/html/colourSchemes/blosum.html. Residue colour depends on whether the residue either matches, or has a positive BLOSUM62 score with, the consensus residue in that column (or residues if there is a tied consensus). There is no direct way to output these scores, but it would not be hard to write a Groovy script to do that. Let me know if you would like me to provide one. I hope that helps! Best regards, 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<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carsta...@dundee.ac.uk<mailto: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> 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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