MAPPER 2.0
==========

Sequence-specific NMR Assignment of Proteins by Global Sequence Mapping

Copyright (c) 2002 by Peter Guntert. 
All rights reserved.


Legal conditions:

Any use of this software is subject to the conditions of the
accompanying license. See the file LICENSE for details.


Installation from source:

1. Type `make'.
2. Copy, if needed, the executable programs 'mapper' and 'graf' 
   to any location you want.


Documentation:
- Example input file 'aldolase.fra'
- Publication:
  Guntert, P., Salzmann, M., Braun, D. and Wuthrich, K. (2000). 
  Sequence-specific NMR assignment of proteins by global fragment 
  mapping with the program MAPPER. J. Biomol. NMR 18, 129-137.
- Usage:
  The program reads its input from standard input and writes its output to standard
  output. Typically, the program is run as follows:

    mapper  < input_file  > output_file

  The input file contains the data from all fragments, and some general parameters.
  The format should follow that of the example input file, `aldolase.fra', and the
  description given therein.

  Running time of the program can vary greatly depending on the number of mapping
  possibilities that have to be checked. If the information content of the input is
  low (i.e. short fragments, many missing chemical shifts) runtime can be VERY long
  since the program always performs an exhaustive search over all possible
  combinations of individual fragment mappings in  order to find global mappings.

  The output consists of four sections (see example output file `aldolase.out'):

  1. A list of all acceptable individual mappings for each fragment. The acceptable
     individual mappings are listed by increasing score (Eq. 1 of the paper).

  2. A table of residue sequence versus fragment number indicating where the
     individual fragments have been placed in the accepted global mappings.

  3. The best global mappings, again listed versus the residue sequence.

  4. Summary tables for the best global mappings, and for the individual fragments.

  In addition, the program writes a file with the fixed file name, `mapper.grf', that
  can be used, in the case of CA/CB chemical shifts, to create a graphical
  representation of the  input data and the best global mapping. This file can be
  converted into a Postscript file  with the help of the program GRAF (included in the
  MAPPER package) using the command:

    graf  < mapper.grf  > mapper.ps


Files: 

mapper.f     MAPPER Fortran-77 source code
graf.f       Auxilliary program GRAF Fortran-77 source code
shifts.lib   Library of chemical shift values
aldolase.seq example sequence input file for MAPPER
aldolase.fra example fragment input file for MAPPER
LICENSE      license conditions
README       this file
Makefile     Makefile for compilation


WWW: guentert.gsc.riken.jp
Email: guentert@gsc.riken.jp
