renum_ppm - Renumber PPM Shift Files (Version 1.0)

Purpose: This program takes two or more homologous sequence chemical shift files and renumbers the amino acids such that the amino acids are directly comparable.

  1. Description
  2. Synopsis
  3. Input Files
  4. Authors


Description

This program is useful if you want to compare chemical shifts of homologous sequences when amino acid numbers are not corresponding. Programs like gsc in the camra suite of programs require this correspondence.

First this program will extract the sequence from each shift file and then format it into an xalign input file. After the alignment is carried out, the shift files are then reconstructed according to the alignment.

Because this program uses a generic parameter set to carry out the alignment, one should use this program carefully especially with remotely homologous sequences. If xalign makes a mistake in the alignment then the only alternative is to rewrite the renum_ppm script so that it waits until the alignment is corrected. Needless to say the intent of this program was for sequences where alignments were pretty much obvious.


Synopsis

	renum_ppm shiftFile shiftFile [shiftFile]...
where "shiftFile" is in PPM format. The output for renum_ppm is each shift file renumbered where the file name is the original shift file name with a ".renum" suffix added.


Input Files

The renum_ppm program can only read input shift files which are in PPM format.

The program translates all 3 letter code amino acids to 1 letter code via the $CAMRA/bin/ppm2seq program. Unrecognized amino acids are ok provided there is enough information for xalign to still get the correct alignment. The program will just treat the atom name field as a string of characters. The "ResId" and "molNum" field values are ignored.


Authors

Authors: Robert Boyko, Wolfram Gronwald, Brian Sykes

Funding for this project has been provided by the Medical Research Council of Canada and the Protein Engineering Networks of Centres of Excellence (Canada).


Last modified: Nov 7, 1996

Robert Boyko - robert.boyko@ualberta.ca