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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Serious question:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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. <span class=SpellE>Clustal</span>),
without the need for a reference alignment? <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I’ve come across several papers & servers via Google
& <span class=SpellE>PubMed</span> but all need reference alignments or are
for protein sequences where structural information is available. The closest so
far is by <span class=SpellE>Ahola</span> et al (<a
href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1687212">http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1687212</a>),
which looks great until you reach the end of the alignment quality section of
the methods and find the sentence ‘By comparing the <span class=SpellE><em><i><font
face=Arial><span style='font-family:Arial'>ConsAAs</span></font></i></em></span><em><i><font
face=Arial><span style='font-family:Arial'> </span></font></i></em>calculated
from the test and reference alignments…’. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>What I’m really looking for is a method that I can
apply directly to the alignments generated by our <span class=GramE>users that
is</span> 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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Any advice would be helpful.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Steve<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'>Bioinformatics Unit: Statistics, Modelling &
Bioinformatics Department<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'>Center for Infections<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'>Health Protection Agency<o:p></o:p></span></font></p>
<p class=MsoAutoSig><st1:City w:st="on"><st1:place w:st="on"><font size=3
face="Times New Roman"><span style='font-size:12.0pt;mso-no-proof:yes'>London</span></font></st1:place></st1:City><span
style='mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoAutoSig><st1:country-region w:st="on"><st1:place w:st="on"><font
size=3 face="Times New Roman"><span style='font-size:12.0pt;mso-no-proof:
yes'>UK</span></font></st1:place></st1:country-region><span style='mso-no-proof:
yes'><o:p></o:p></span></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt;mso-no-proof:yes'><a
href="http://www.hpa.org.uk/cfi/bioinformatics/index.htm"><span lang=DE
style='mso-ansi-language:DE'>http://www.hpa.org.uk/cfi/bioinformatics/index.htm</span></a></span></font><span
lang=DE style='mso-ansi-language:DE;mso-no-proof:yes'><o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=DE
style='font-size:12.0pt;mso-ansi-language:DE'><o:p> </o:p></span></font></p>
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