$Id: README,v 1.4 2002/07/13 08:52:13 bannai Exp $
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                          caml-iPSORT
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PLEASE READ THE LICENSE AVAILABLE AT
		 http://biocaml.org/ipsort/
FOR TERMS OF USAGE.

Introduction ---------------------------------------------------------
iPSORT is a predictor for N-terminal protein sorting signals. 
Given an input sequence, it will predict whether the sequence has:
	1. Signal peptide
	2. Mitochondrial Targeting peptide
	3. Chloroplast Transit peptide
	4. Other (none of the above)

It will also output some values which were calculated for the
sequence, according to the simple rules that iPSORT is based on.

The original web version is located at
	 http://hc.ims.u-tokyo.ac.jp/iPSORT/

Installation ---------------------------------------------------------
  Just put the binary in a directory in your path.
  You must obtain a license key at the ipsort web site,
  and put it under your home directory. (e.g. /home/username/.ipsort-license)

  (You can put the license key in a different place if you specify the
   file with -l option)

Usage ----------------------------------------------------------------

> ./ipsort [options]
Usage: ./ipsort
  -l specify location of license file (default: ~/.ipsort-license)
  -type set type of protein. `plant' or `nonplant' (default is `plant')
  -i name of file for input (default, or "-" is stdin)
  -F assume FASTA format for input
  -o name of file for output (default, or "-" is stdout)
  -v print version and exit
  -help  display this list of options
  --help display this list of options

By default, caml-ipsort will read the standard input. For each line of
standard input, it will output a prediction for the sequence. If -F is
specified, the input will be assumed to be in FASTA format, that is
like:

> Some name
SEQUENCEHERESEQUENCEHERE
SEQUENCEHERESEQUENCEHERE
> Next name
SEQUENCEHERESEQUENCEHERE
SEQUENCEHERESEQUENCEHERE

Sample Output:
======================================================================
Input Sequence:
        MALLQSRLLLSAPRRAAATARASSWWSHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKSYVLNCVRKAEAMI...

Prediction:
        Mitochondrial Transit Peptide

Values used for prediction:
        ---------
        substring [6,25]; average Hydropathy index (Kyte-Doolittle, 1982) = -0.115000 >= 0.922500 ? NO
        ---------
        substring [1,30]; average Negative charge (Fauchere et al., 1988) = 0.033333 < 0.083000 ? YES
        substring [1,30]; pattern: 22121222; mismatch: (2,{sub=false; ins=true; del=true}); match: YES
                          MALLQ-SRLLLSAPRRAAATARASSWWSHVE
                          22222-2122222211222221222222020
                             22121222
        ---------
        substring [1,30]; average Isoelectric point (Zimmerman et al., 1968) = 6.508000 >= 0.621000 ? YES
        substring [1,15]; pattern: 100100110; mismatch: (3,{sub=false; ins=true; del=true}); match: YES
                          MA-LL-QS-RLLLSAPRR
                          00-00-00-100000211
                            100100110
======================================================================

"Values used for prediction" shows the values when tracing the
decision list of iPSORT (http://biocaml.org/ipsort/iPSORT/how.html).


More Information -----------------------------------------------------
caml-iPSORT is written in the OCaml language and is linked with part
of the OCaml standard library (Copyright INRIA, licensed under LGPL
but with special exceptions on linking).

OCaml      : 	http://caml.inria.fr/
caml-iPSORT:	http://biocaml.org/ipsort/
BioCaml    :	http://biocaml.org/

Authors --------------------------------------------------------------
Copyright 2001
Hideo Bannai (bannai@ims.u-tokyo.ac.jp)