[ssml] Assess sequence alignment quality without reference alignments?

[Mensur Dlakic]

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:
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>Is this list still active? I’ve 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?
>
>
>
>I’ve 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 I’d like to get some thing that examines the alignment 
>more directly.
>
>
>
>What I’m 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 I’m 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
>
>
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==========================================================================
| 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        |
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