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<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: 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 [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<mailto: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<mailto: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<mailto: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<mailto:g.j.bar...@dundee.ac.uk> Tel: +44 1382 385860 | www.compbio.dundee.ac.uk<http://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
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