[ssml] Assess sequence alignment quality without reference alignments?

Mensur Dlakic mdlakic at montana.edu
Fri Jul 27 11:06:10 EDT 2007


Hi Steve,

Such a thing most definitely exist, at least for protein sequences. I'm not 
sure exactly what you are looking for because you ask for the assessment of 
_nucleotide_ multiple sequence alignments, yet below you gave an example 
for protein multiple alignments. Either way, type Poch O or Thompson JD 
(better yet, both) into PubMed and you will have plenty to read. In 
particular, look at articles with PMID numbers 11734009 and 12801878 or 
just type "norMD align" into any search engine.

SAM ( http://www.soe.ucsc.edu/compbio/sam.html ) has a function that 
improves the existing alignments of _protein_ sequences while removing 
unrelated entries, but it is fairly slow.

Finally, if you are looking only for nucleotide alignments, as stated, I 
suggest you contact the experts directly - Oliver Poch and Julie Thompson 
certainly come to mind.

Best regards,

Mensur


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          |                                    |
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