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# FILE   : README
# AUTHOR : Jens Stoye, Constantin Bannert
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#
# 2000/05/26: Inital version (Jens).
# 2002/01/31: Added documentation for jscan (Conni).
# 2002/10/23: Updated link to WWW home page (Jens).
#
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This distribution contains three executables:

jali:    This program takes as input a protein sequence and a multiple
         alignment of a protein family and computes a jumping alignment
         of the sequence and the alignment.

jsearch: This program takes as input a protein database and a multiple
         alignment of a protein family, compares all proteins from the
         database to the alignment, and then outputs the database in sorted
         order with respect to the computed jumping alignment score.
	 
jscan:	 This program takes as input a protein sequence and a database of
	 multiple alignments of protein sequences (PRODOM format).
	 jscan computes a jumping alignment for the sequence and each
	 multiple alignment from the database; and then outputs the cluster
	 names with the associated score, respectively.

All sequence, alignment and database input requires FASTA format, except the
database for jscan, which requires the PRODOM format.


USAGE

> jali [options] sequence.fasta alignment.fasta
> jsearch [options] sequence-db.fasta alignment.fasta ...
> jscan [options] sequence.fasta alignment-db.prodom

Options:
  -w weights_filename      //amino acid similarity matrix (default: vt160)
  -i gap_initiation_cost   //must be smaller or equal to zero (default: -24)
  -e gap_extension_cost    //must be smaller or equal to zero (default: -6)
  -j jump_cost             //must be smaller or equal to zero (default: -22)
  -f format_ID             //output format: 0:ASCII (default)  1:HTML
                           //               2:HTML double-spaced
  -p                       //print alignment (jali only)
  -o                       //run in verbose mode
  -v                       //print version
  -h                       //print this help message


INSTALLATION

First, unwrap the package. On the UNIX prompt type

> gunzip jali-VVV.XXX.tar.gz
> tar xvf jali-VVV.XXX.tar

where VVV is the current version of JALI and XXX is your operating system.
This will create a directory "jali-VVV.XXX" containing the executables.
You might want to include this directory in your PATH environment.


TESTING

To test your installation of jali, cd into the jali-VVV.XXX directory and
type the following:
 
> jali sample_sequence sample_alignment

The output of the program should be:

44

To get the actual alignment, type:

> jali -p sample_sequence sample_alignment

To test the correct installation of jsearch, type:

> jsearch sample_sequence_db sample_alignment

The output of the program should be a list of the 19 database sequences with
a score at the end of each line (the higher the score, the better fits the
database sequence into the family represented by the sample_alignment).

To test the correct installation of jscan, type:

> jscan sample_sequence sample_alignment_db

The output of the program should be a list of the 18 database alignments
included in the 'sample_alignment_db' with a score at the end of each line
(the higher the score, the better fits the sample_sequence into the family
represented by the respective alignment).



FURTHER INFORMATION

For further information please consult the JALI WWW Home Page:

              http://bibiserv.techfak.uni-bielefeld.de/jali/

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