Jeff, We do not have the thermodynamic parameters for methylated CG nearest neighbors. I suppose they could be determined from delta Tm, but we would, of course have to assume that the cytosine residues of all CG neighbors were methylated. No. That is incorrect. They would be specified when the sequence is read in. Actually this question is almost trivial, but we would need the enthalpy and entropy values as a function of ionic strength. I am very much in the middle of something, so if you have the time could you look through the literature. No way am I going to measure them. I think my apparatus is kaput now anyway. dick were meth At 10:33 PM 11/30/00 +0000, you wrote: >Received: from www.bioinformatics.org [129.63.144.25] by mercury.capeonramp.com > with ESMTP (SMTPD32-6.00) id ACE915D00D4; Thu, 30 Nov 2000 12:22:49 -0500 >Received: from genet.sickkids.on.ca > (violin.genet.sickkids.on.ca [207.176.225.114]) by www.bioinformatics.org > (8.9.3/8.8.7) with SMTP id NAA28355 for <jeff at bioinformatics.org>; Thu, > 30 Nov 2000 13:30:42 -0500 >Received: from genet.sickkids.on.ca ([142.20.155.178]) > by genet.sickkids.on.ca (8.8.8/8.8.8) with ESMTP id MAA09406 for > <jeff at bioinformatics.org>; Thu, 30 Nov 2000 12:24:03 -0500 (EST) >Date: Thu, 30 Nov 2000 12:28:58 -0500 >From: "Dr. Christopher Pearson" <cepearson at genet.sickkids.on.ca> >Subject: methylation? >To: jeff at bioinformatics.org >Message-id: <3A268E55.C6C5FDF5 at genet.sickkids.on.ca> >MIME-version: 1.0 >X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) >Content-type: text/plain; x-mac-creator=4D4F5353; x-mac-type=54455854; > charset=us-ascii >Content-transfer-encoding: 7bit >X-F: <cepearson at genet.sickkids.on.ca> Thu Nov 30 12:22:50 2000 >X-Accept-Language: en >X-RCPT-TO: <bizzaro at geoserve.net> > >To: Jeff >From: Christopher E. Pearson, Ph.D. (cepearson at genet.sickkids.on.ca) >Date: November 30, 2000 > >Jeff, > >I was wondering if the Meltism program can account for melting >differences due to meCpG status. Methylation of C residues greatly >increases the melting temperature of DNAs (Ehrlich,M et al., 1975, >Biochim. biophys. Acta, 395:109-119; Collins,M. & Myers,RM 1987, J. Mol. >Biol. 198:737-44). If Meltism does not permit for this variation can it >be modified? Are there other programs that may be able to perform such >an analyses? Thank you in advance for your assistance on this. > >Christopher >*********************************************************** >Christopher E. Pearson, Ph.D. > >Hospital for Sick Children tel: (416) 813-8256 (office) >Department of Genetics tel: (416) 813-8170 (lab) >555 University Avenue tel: (416) 813-6384 (secretary) >Elm Wing, Rm. 11-135 fax: (416) 813-4931 >Toronto, Ontario email: cepearson at genet.sickkids.on.ca >Canada M5G 1X8 > > >