Rhone-Alpes Bioinformatics Center



- 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.

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