Hi. I have to say I'm embarrassed by this one, but then, that's life. The error has been in the code since the dawn of time, it seems!
On 03/02/2017 09:28, Geoff Barton wrote: > BLOSUM62 should be symmetrical, so that is is a typo. [sic] :) Mungo - may I suggest that rather than simply fixing the typo, we: 1. Provide a legacy option allow the broken BLOSUM62 matrix to be used in place of the real matrix. (see, e.g. https://issues.jalview.org/browse/JAL-728 ) 2. Move the score matrices out of static initialisers into flat files under resources, either as the NCBI matrix format or the aaindex format: http://www.genome.jp/dbget-bin/www_bget?aaindex:HENS920102 (there might not be an issue about importing AAindex matrices yet..) > On 03/02/2017 09:17, Mungo Carstairs (Staff) wrote: >> Is this a typo? I thought pairwise scoring has to be symmetric (PAM250 >> matrix is). Not sure that holds in general (there's no requirement in biology for it, and most alignment methods don't depend on it). Log odds matrices as formulated by Henikoff & Henikoff are symmetric, however. >> The help page for PCA says that the Jalview mode calculation (e.g. >> using BLOSUM62) creates an asymmetric score matrix. Is that correct, I guess that's just a knock on effect. However, it's not really relevant - the 'Jalview mode' is the variant of the seqspace algorithm first provided by Jalview. I discovered we were doing something different to the original method back in 2012: https://issues.jalview.org/browse/JAL-1125 >> or is it actually symmetric (if the score matrix also is)? perhaps you can verify ? Thanks again for your eagle-eyed exhaustive testing, Mungo! Jim. -- ------------------------------------------------------------------- Dr JB Procter, Jalview Coordinator, The Barton Group Division of Computational Biology, School of Life Sciences University of Dundee, Dundee DD1 5EH, UK. +44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
