Dear  All,
Below are the replies I received on the questions regarding DCSE and
18S rRNA alignments.
Firstly, I was stuck by the amount of replies both those containing
suggestions and those who simply said that they were in the same
situation. Thank you all!

My feeling about it is that all those zoologists/botanists ( i.e. not
biochemists or computer programmers) who are working with phylogenetic
studies and use rRNA as their target gene need to get together and
work out one system to which all those multiple utilities packages and
scripts could be adjusted - otherwise they are all lost in
translation. Perhaps this will be my next project. Meanwhile I have
tried to compile some main answers I had received from you in the
order I asked the questions.

Please feel free to contact me if you need any additional information.

1) does anyone know if this software is still in use and if yes where
I can get it?
DCSE has probably migrated to van der Peer's new location in Belgium,
the Antwerp lab having closed and its members dispersed.
One person send me a ink to download DCSE from China.
http://www.cbi.pku.edu.cn/ftp/ftp-a-d.html

Many of you suggested that DCSE should not be used for various reasons
such as compatibility of data format, inability to run it ( well I am
not surprised - it seems to have been written in the days of Sun
Microsystems rule), and general dislike of the package. I have
downloaded it and could not install it on BSD or Fedora.

2) if there is an alternative package which can read/edit of assist in
alignment of rRNA with secondary structure (i.e. what do YOU use?)

Here the list of packages people suggested to use. Please note that
none of the packages can actually align the sequences for you ( apart
from ARB see: http://www.arb-home.de/) I have tried ARB (for quite a
long time before -  it is an excellent and very complex package
designed originally for 16S rRNA) but I have some problems making it
work with my sequences.
See Dave Kysela's excellent tutorial on ARB:
http://www.mm.helsinki.fi/users/GJURGENS/Arb/ARB_tutorial.htm
If you want to go ahead with ARB - it may be difficult to install on
MAC OS X as the manual on the web site is outdated - contact me, I
have done it a few times by now. Also LINUX installation is a bit
scary as ARB looks for old libraries which you need to link manually -
again contact me if you are stuck.

Other packages( these just let you edit RNA in a nice way):
You can access the application at the following address:
http://4sale.bioapps.biozentrum.uni-wuerzburg.de/
jRNA pages http://hymenoptera.tamu.edu/rna
Some Perl scripts for conversion http://bioinformatics.org/paradise/
SARSE (http://sarse.kvl.dk/).
PHASE (has some scripts and links) www.bioinf.manchester.ac.uk/resources/phase/
Max Telford has some scrips: Xstem Ystem to extract data from DCSE RNA
database depository online. The scripts are availiabl;e from the
author only see his paper:
Telford, M. J., M. J. Wise, et al. (2005). "Consideration of RNA
secondary structure significantly improves likelihood-based estimates
of phylogeny: Examples from the bilateria." Molecular Biology And
Evolution 22(4): 1129-1136.

3) if any of you came across any good "practical" guide on how
to do the secondary structural alignment for 18S rRNA, whether it is "by
hand" or computer software assisted.
This is easy to answer there is only one guide, which I found rather
useful to start with:
http://hymenoptera.tamu.edu/rna/methods.php

The above seem to be the amalgamation of all answers I got I am sorry
if I forgot anyone.

Consequently, I ended up trying to make ARB work and also doing in
parallel a manual alignment based on the published structure. It is
very time consuming, but after a few days of staring at 4 colored
nucleotides on the screen the world seems so multicoloured I am almost
enjoying it. :-)))

Anton Tsyganov
mailto:atsyganov@gmail.com
mailto:bsatsyganov@swansea.ac.uk

atsyganov@gmail.com