Aline - Protein Sequence Editor

Aline
An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures

Charlie Bond (email) and Alex Schüttelkopf
Latest Version 011208
Please cite "Bond, C.S. and Schüttelkopf, A.W. (2009), Acta cryst. D65, 510-512" [CLICK HERE FOR REPRINT]

Synopsis:

Aline is an interactive perl/tk application which can read common sequence alignment formats which the user can then alter, embellish, markup etc to produce the kind of sequence figure commonly found in biochemical articles.

Prerequisites, Download and Installation:

Download the latest version of Aline here: [tar-gzip] or [tar-bzip2] or [zip]
Aline is a perl program requiring at least perl 5.8 and the Tk module.

Perl: Recent linux and MacOSX distributions include perl/Tk so you should be ready to go, or they can be installed via a package manager (e.g. ubuntu: "apt-get install perl-tk"; MacOSX with fink: "fink install tk-pm588"; Windows with ActivePerl 5.10+: "ppm install Tk" in a CMD window). See below for generic instructions for installing the perl Tk module in an existing perl installation.
(Thanks to Andreas FÃ¶rster, Mads Gabrielsen and Joel Mackay for some tips).
If you have trouble with perl (and especially if you use windows), you can install the free ActivePerl distribution which includes ppm package manager with which you can install Tk. If you have insurmountable problems under Windows, Aline will also work under the CygWIN environment (you need to ensure that perltk, xorg-x11-base and gs are all selected for installation).

Brief Instructions

Windows:
(1) Ensure ActivePerl is installed (see above).
(2) Download and unzip the zip file.
(3) Open the "aline"->"bin" folder and double-click "aline.pl" (or "aline" with the ActivePerl logo).

Unix/MacOSX:
(1) Open a terminal window
(2) Download the bzip2 or gzip file.
(3) Unpack somewhere: e.g.
cd /programs/
gzip -dc /downloads/aline.tar.gz | tar -xvf -
(4a) Setup use for tcsh/csh users: (type 'echo $SHELL' to find out which shell you use)
setenv ALINEHOME /programs/aline
set path = ($path $ALINEHOME/bin)
rehash
The 'setenv' and 'set path' lines can be added to your ~/.tcshrc or ~/.cshrc file to automatically setup aline when you log in
(4b) Setup use for bash users: (type 'echo $SHELL' to find out which shell you use)
ALINEHOME=/programs/aline ; export $ALINEHOME
set PATH=$path:$ALINEHOME/bin ; EXPORT $PATH
The 'ALINEHOME' and 'PATH' lines can be added to your ~/.bashrc file to automatically setup aline when you log in

(5) Type 'aline' and start playing. To get full functionality, a number of accessory programs are desireable:

Ghostscript (commonly installed on linux/MacOSX - type 'gs' in a terminal to test), otherwise see if it is available as part of your system or go to http://pages.cs.wisc.edu/~ghost/
wget http://www.gnu.org/software/wget/ - already there with most linux/osx. Make sure 'wget' is in your path.
DSSP http://swift.cmbi.ru.nl/gv/dssp/: install and make sure 'dssp' is in your path.
CLUSTALW ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW//: install and make sure 'clustalw' is in your path.
CHAINSAW http://www.ccp4.ac.uk/ccp4/html/chainsaw.html - part of the CCP4 suite. Install CCP4 and make sure 'chainsaw' is in your path.

Installing perl and its modules

NOTE:If you have problems with perl prerequisites (compilation, installing etc), please consider using ActivePerl (see above). To install additional modules using a prexisting perl version you must have superuser or root privileges. In principal, the Tk module can be installed by issuing the command "perl -MCPAN -e 'install Tk'". However, as Tk provides a graphical user interface, the X display must be set up to allow windows to be created during the build process, so it may be necessary to login as root via ssh ('ssh -X root@localhost') rather than '/bin/su -'.

Quickstart:

Assuming ALINEHOME is set and aline is in your path, just type 'aline' to start it.
A window will appear with a menubar at the top, a control panel on the left and a canvas on the right. Use File->Load Sequences... to load an alignment in any common format. You are then ready to play with the various actions and adjustments from the Actions section of the control or the menubar. Aline was conceived to be reasonably intuitive. We hope to add documentation for specific features when time permits. (Contributions from users are happily invited!).

Detailed Description:

When time permits ...