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Article #2230Re: GCG V. 9.0-GAP
From: Cedric Govaerts
Date: Tue, 27 May 1997 00:00
Date: Tue, 27 May 1997 00:00
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In article <5mdbsh$ec0@netnews.upenn.edu>, ellis@vesicle.dental.upenn.edu says... > > >As indicated below, the scoring matricies are indeed the problem. A simple solution is to add the >following to your gap commands: -matr=oldpep.cmp. This uses the version 8 matrix, and gives the >same fits as version 8. > >Ellis Golub > But the renormalized matrix used by GCG 8 has no scientific value, because a conserved Glycine is in fact different than a conserved Tryptophan.. Better use Blosum 62 or PAM 250 (not renormalized !!). Cedric Govaerts
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X-Google-Language: ENGLISH,ASCII-7-bit X-Google-Thread: 103fe7,972e8e1723c718b2 X-Google-Attributes: gid103fe7,public X-Google-Thread: fa6b6,972e8e1723c718b2 X-Google-Attributes: gidfa6b6,public From: cgovaert@ulb.ac.be (Cedric Govaerts) Subject: Re: GCG V. 9.0-GAP Date: 1997/05/27 Message-ID: <5me8vi$ngj@rc1.vub.ac.be> X-Deja-AN: 244201494 References: <33893C87.446B@cc.huji.ac.il> <33898FA4.FF6@caos.kun.nl> <5mdbsh$ec0@netnews.upenn.edu> Organization: ULB Newsgroups: bionet.software,bionet.software.gcg