question about scoring a multiple sequence alignment 7-21-14

2014-08-29

question about scoring a multiple sequence alignment 7-21-14
score msa

email
https://mail.google.com/mail/u/0/?ui=2&shva=1#search/hamish/147582100da767ff
{

Hi,

> Is there a way that I can view a single quantitative score that
> indicates the quality of a multiple sequence alignment in Clustal
> Omega?  If there is not, perhaps I could quickly calculate it from the
> resulting output matrix?  Thanks for any help and information you have
> to offer!

Assessing alignment quality is an active area of research. I suggest you search the web and the literature for possible tools and try them on your alignment to assess which will work for your case. See:

https://www.google.com/search?q=alignment+quality+score
http://europepmc.org/search?query=multiple%20alignment%20quality%20score

All the best,

Support@EMBL-EBI

}

Note that later on I found the following page which describes some methods for scoring a multiple alignment
-http://www.incogen.com/bioinfo_tutorials/Bioinfo-Lecture_4-multiple-sequence-align.html
{
-scoring functions
--minimum entropy
--sum of pairs
}

-Here's a paper on the topic
--A statistical score for assessing the quality of multiple sequence alignments
---http://www.biomedcentral.com/1471-2105/7/484/
---I quickly looked through this paper, but I could not see any link to download a program which would calculate the score they describe

-Here's another paper on the topic
--Accuracy estimation and parameter advising for protein multiple sequence alignment.
---http://europepmc.org/abstract/MED/23489379;jsessionid=psBi38zqkI6704XyA71Y.11

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