The program MASIA (Multiple Aligned Sequences Investigation and Analysis) searches for consistent patterns in multiple aligned sequences. Predictions of secondary structure and inside/outside properties of residues at any point in the sequence alignment are based on generalized rules for globular proteins based on observations from known three dimensional structures of proteins that have indicated certain amino acids are more likely to occur in -helix, turn, or-sheet regions. The secondary and tertiary structure of a protein is related to the chemistry of the individual amino acid residues, but a clear picture of the secondary structure may not be apparent for one protein sequence alone. Comparing many aligned, related sequences can reveal patterns of sequence conservation that indicate the location of residues essential for the function, folding or solubility of the protein.

The rules are manipulated as corresponding combinations of commands for predicting specific properties. Users can easily extend or create new rules for their specific purposes. Before using MASIA, the best possible alignment of the protein with other proteins in the SWISS-PROT data base should be obtained. MASIA uses as input files generated with PileUp or ClustalW. However, alignments done with other programs can be adapted to the output format of these programs.

This manual describes graphic user interface of MASIA, format of input and output files, the command structures, methods, and examples of how to run the program.

Comments, suggestions and reports on bugs are welcome. Please send them to

The program can also be obtained via FTP. Please inquire further information from Dr. W. Braun.