Hello Rohit,
I've attached a groovy script that can be run to produce average hydrophobicity score annotation (copying in the list now we know it works for you!). Tools | Groovy console | paste in the script and Script | Run. I recommend choosing Jalview option Annotations | Autocalculated annotation | Show Last, so the new annotation stays above the others. To answer your follow-up questions: You can extract the annotation score values as CSV by right-click on the label at the left, option Export Annotation. This works for all rows including the new Hydrophobicity scores. You can copy the consensus sequence to the clipboard by right-click on 'Consensus' and 'Copy Consensus Sequence'. See http://www.jalview.org/help/html/menus/alwannotationpanel.html. You can increase the font size of your alignment from the Jalview Format | Font menu. Let us know if you have any more questions, and happy Jalviewing! Kind 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 Dr. Rohit Jain <rohit.mpi...@gmail.com> Sent: 22 March 2019 02:15:48 To: jalview-discuss@jalview.org Subject: [Jalview-discuss] How to plot hydrophobicity in multiple sequence alignment Hi everyone, I really like Jalview. It could show hydrophobicity of my aligned amino acid sequences. The number of aligned sequences is large. It will help to have average hydrophobicity at every position For all the aligned seuqnces. How can color scheme be converted to hydrophobicity score ? Jalview colors every aa based on its hydrophobicity. Can I access the numbers behind colors ? I have attached one of my result. Please help. Best, Rohit Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 The University of Dundee is a registered Scottish Charity, No: SC015096
hydrophobicityScores.groovy
Description: hydrophobicityScores.groovy
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