ESPript, Easy Sequencing in Postscript, is a utility to generate
a pretty PostScript output from aligned sequences.
Key Features
ESPript is a utility, whose output is a PostScript file of aligned
sequences with graphical enhancements. Its main input is an ascii file
of pre-aligned sequences. Optional files allow further rendering. The program
calculates a similarity score for each residue of the aligned sequences.
The output shows:
-
Secondary Structures
-
Aligned sequences
-
Similarities
-
Consensus
-
Accessibility
-
Hydropathy
-
User-supplied markers
-
Intermolecular contacts
In addition, similarity score can be written in the bfactor column of a
pdb file, to enable direct display of highly conserved areas.
Reference article is: Gouet, P., Courcelle, E., Stuart, D.I. and Metoz,
F. (1999). ESPript: multiple sequence alignments in PostScript. Bioinformatics.
15
305-308
Installing ESPript
ESPript.f is a one-file FORTRAN program, available via ftp anonymous at
ftp.ipbs.fr
You can compile the source by using the Makefile. Just type
:
make
By default, the binary is placed in the bin directory. The
program has been tested under Unix, Linux, VMS and Win32.
ESPript can be executed using a standard input or a html form.
Help
and Tutorial are available. Most functions are shown on examples.
If you want to install the script of the html interface on your
server (Unix or Linux-Apache), please read the installation
documentation.
Running ESPript via the web
To run the program from this server, press the red button and fill
the form. Then, you just have to click to receive, and possibly display,
the output PostScript file and optional pdb file. You can also convert
the PostScript to GIF or TIFF files via the interface (this uses an external
conversion program, for instance the program convert).
You may have to configure your browser with appropriate helpers applications
to display the generated output. The mime type of the postscript file is
application/postscript,
it could be linked to ghostview.
The mime type of the pdb file is chemical/x-pdb, it could be linked
to rasmol
Main site is
Institut de Pharmacologie
et de Biologie Structurale, Toulouse, France.
Mirror sites are Columbia
University Bioinformatics Centre, New York,
USA, Bioinformatics Centre,
Singapore and the
Infobiogen server, France.
ESPript: the calendar
Acknowledgments
We wish to thank Dr Richard Wade, Institut
de Biologie Structurale, Grenoble, and Pr David Stuart, Laboratory
of Molecular Biophysics, Oxford, where this program was developed
firstly. The program is now harbored in sunny IPBS,
Toulouse. Catherine Mazza, EMBL, Grenoble and Jean-Denis Pédelacq,
IPBS, Toulouse, helped to test the program.
Authors
ESPript was created by Patrice Gouet
and Frédéric Metoz.
Emmanuel Courcelle wrote the html-user
interface.
The calendar is a masterpiece of Michel Gouet.
Please join ESPript.list
and send your messages to espript@ipbs.fr,
if you have questions, suggestions or if you want to be informed about
program releases.
Copyleft This software
is covered by the gnu public license.
