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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> smith-waterman https://forum.ugene.net/forum/YaBB.pl?num=1355843226 Message started by randolf on Dec 18^th, 2012 at 10:07pm

Title: smith-waterman
Post by randolf on Dec 18^th, 2012 at 10:07pm

Hi,
I have the latest version of Ugene 1.11.3, 64 bit, the linux version.

I want to do a Smith-Waterman search, but I can not search with all the algorithms and matrices as listed in the manual. As algorithm I can only chose between Classic 2 and SSE2 and as scoring matrices only dna, rna and nuc 4.4. this is strange to me, because as written in the manual, in the $UGENE\data\weight_matrix directory I have many more weight matrices.

Help will be greatly appreciated!
Thanks,
Thomas

Title: Re: smith-waterman
Post by Yuriy Vaskin on Dec 19^th, 2012 at 6:29pm

Hello,
thank you for your question!

The list of matrices is determined by the alphabet of a sequence. If your sequence has nucleic alphabet only those matrices that you listed in your post are available. Protein substitution matrices don't make sense in nucleic sequences, that is why they are available only for sequences with amino alphabet.

You can add your own matrix in the folder, but it should be in the same format as the others.

Title: Re: smith-waterman
Post by randolf on Dec 21^st, 2012 at 3:48pm

Actually, thats kind of logic. Don't know why I couldn't think of that by myself. Thanks for your hint!
Thomas