Clarification needed please.
Jalview's BLOSUM62 matrix is nearly but not quite symmetric: C -> R scores -3 (ResidueProperties.BLOSUM62[1, 4]) R -> C scores +3 (ResidueProperties.BLOSUM62[4, 1]) (help page shows this the other way round - I think) Is this a typo? I thought pairwise scoring has to be symmetric (PAM250 matrix is). The help page for PCA says that the Jalview mode calculation (e.g. using BLOSUM62) creates an asymmetric score matrix. Is that correct, or is it actually symmetric (if the score matrix also is)? Thanks 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> [email protected]<mailto:[email protected]> [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 The University of Dundee is a registered Scottish Charity, No: SC015096
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