Liwei. I have forwarded your question to the user group - you sent it to
the email of the list owner.
Liwei Zhou wrote:
Does version 2.4 still treat DNA alignment each symbol as amino-acid rather than a nucleotide?
I am not sure which area you mean here, but generally the answer is no -
unless the user selects an amino acid based colouring or analysis
explicitly.
If the alignment contains sequences which are predominantly ACGT or U,
jalview will not show conservation and BLOSUM 62 quality annotation
scores, and will use a DNA substitution matrix for computing pairwise
alignments. However, it does not disable any option where BLOSUM 62 is
explicitly used (calculating trees or for PCA, or BLOSUM colouring) -
likewise with the conservation colouring (which is again, based on amino
acid properties). Finally, alignment type is not taken into account in
the web services menu, either: only clustalW and MAFFT properly cope
with DNA sequences (this is shown in the log of the job), Muscle aligns
DNA with a protein matrix, and JNet will also give erroneous results for
a DNA sequence or profile.
I hope this helps
Jim Procter.
ยทยทยท
--
-------------------------------------------------------------------
J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.