PS Below is the link for DNA and RNA Alignment Tuneup page http://www.soe.ucsc.edu/compbio/HMM-apps/tuneup-dna.html At 04:32 AM 7/27/2007, you wrote: >Content-class: urn:content-classes:message >Content-Type: multipart/alternative; >boundary="----_=_NextPart_001_01C7D039.5E9D2F84" > >--> > >Is this list still active? Ive not heard anything here since the end of >last year, but hey maybe we all know what we need and have kept quiet. > > > >Serious question: > >Is there an algorithm / method / program or server that can assess the >quality of a nucleotide multiple sequence alignment (generated by a >progressive clustering algorithm e.g. Clustal), without the need for a >reference alignment? > > > >Ive come across several papers & servers via Google & PubMed but all need >reference alignments or are for protein sequences where structural >information is available. The closest so far is by Ahola et al >(<http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1687212>http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1687212), >which looks great until you reach the end of the alignment quality section >of the methods and find the sentence By comparing the ConsAAs calculated >from the test and reference alignments . > >The ability to bootstrap trees generated from alignments is already well >established and Id like to get some thing that examines the alignment >more directly. > > > >What Im really looking for is a method that I can apply directly to the >alignments generated by our users that is better than a simple set of >column conservation scores across the alignment but Im starting to >think that such a thing does not exist. > > > >Any advice would be helpful. > > > >Steve > > > >Bioinformatics Unit: Statistics, Modelling & Bioinformatics Department > >Center for Infections > >Health Protection Agency > >London > >UK > ><http://www.hpa.org.uk/cfi/bioinformatics/index.htm>http://www.hpa.org.uk/cfi/bioinformatics/index.htm > > >_______________________________________________ >ssml-general mailing list >ssml-general at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/ssml-general ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic at montana.edu | ==========================================================================