MAPPER 2.1
==========

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.txt for details.


Installation from source:

1. Type `make'.
2. Copy, if needed, the script 'mapper' 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

  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. 

  The program will produce an output file with the same name as the input file but 
  extension .out, and a plot file in PDF format if the command ps2pdf is available 
  on the system, or in Postscript format otherwise.

  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.

  The additional plot file provides, in the case of CA/CB chemical shifts, a 
  graphical representation of the input data and the best global mapping. 


Files: 

mapper       script to start MAPPER, can be copied to any desired location
mapper.f     MAPPER Fortran source code
graf.f       auxilliary program GRAF Fortran 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.txt  license conditions
README.txt   this file
Makefile     Makefile for compilation


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