Introduction
MPSA is a software intented to the protein
sequence analysis. It provides many methods and tools integrated in a graphical user interface
available on several operating systems.
MPSA can search homologous proteins in protein sequence databases like
SWISS-PROT,
trEMBL, or NRL3D. These proteins are identified using FastA or PattInProt (a method that
we developed which searches amino acid patterns in protein sequence databases). The
alignment of homologous proteins subset can be made with Clustal W, MPSA provides a
graphic window to set the alignment parameters.
Secondary structure prediction performed
with several methods can be included in the alignment. The methods are available either in
local mode from within the package (Homologue method Levin, directional information
methods such as Gibrat and GOR) or through the internet (DPM and SOPMA available on
our Web server,
and the PHD method available on the
PredictProtein
server).
Prosite site and signature search is an other useful method for protein sequence analysis which
can be made from within MPSA.
Physico-chemical profiles like hydrophibicity, antigenicity,
flexibility, solvent accessibility, etc can be performed and displayed in a graphical window.
Several tools included in MPSA simplify the analysis of protein sequences. Our
program reads and writes sequences in the most used sequence formats: Pearson/FastA,
EMBL, etc. Multiple alignment editor provides gap insertion/deletion with immediate update
of the alignment display. Identity and homology overviews show as graphs analyze the
alignment quality. Primary or secondary structures can be moved up and down with the
mouse from one position to an other. A find tool searches character pattern in the displayed
structures. Several color codes are available in order to outline different properties of the
primary or secondary structures. Dialog windows gives information to the user about the
current action.
MPSA is a window-based user interface available on UNIX-like operating system
(tested on IRIX 5.xx 6.xx, AIX 3.xx 4.xx and Solaris) and on Macintosh.
