MASIA 2.0

Multiple Aligned Sequences Investigation and Analysis

Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
[MASIA] [MANUAL] [SCSB][UTMB] [CONTACT]
MASIA searches for consistent patterns in multiple aligned sequences. Predictions of secondary structures and inside/outside properties of residues at each position in an aligned sequences are based on generalized rules for globular proteins, which are derived from observations of known 3D-structure of proteins. The secondary and tertiary structure of a protein is related to chemical characterisitics 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 macros (i.e., corresponding combinations of commands) to predict specific properties. Before using MASIA, the best possible alignment of the protein with other proteins in the SWISS-PROT database should be obtained. MASIA uses as input files generated with PileUp or ClustalW. The simplified applications can be directly accessed through this form. An on-line manual is available. Comments are welcome, please mail them to Werner Braun.

Try the multiple aligned sequences example in ClustalW format or example in PileUp format.
File name for mutiple aligned sequences in ClustalW (*.aln) or PileUp (*.msf) format:
CLUSTAL PILEUP Relative Entropy Cutoff:  Valid only for PCPM
Length Cutoff:  Valid only for PCPM
 Max. Gap Cutoff:  Valid only for PCPM
Select desired macro to run the program:
    If error, check the manual
ADVANCED OPTIONS
Check this box to use the following macro. If selected, it will override the previous selected macro.
The text area to edit the macro for your applications:
This is the library that defines properties for each individual amino acid. You may add new properties here for your applications. For details, please refer the manual.

  • Acknowledgements

    • An internal error was detected in the service software. The diagnostics are being emailed to the service system administrator (venkat@bohr.utmb.edu).