# This is part of method for:
# Amin Zia and Alan M Moses, "Ranking insertion, deletion and nonsense mutations based on their effect on genetic information", BMC Bioinformatics 2011, 12:299.
# See (http://www.moseslab.csb.utoronto.ca/amin/indelz.html) for a web-based interface to the program. 
# Comments or questions: Amin Zia (amin.zia@utoronto.ca)
# July 2011

INTRODUCTION:
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Indelz is a simple perl script to perform the following:

- Prepare the input FASTA cDNA sequence
- Translate the sequence into the corresponding amino-acid sequence
- Genenrate multipe-sequence protein alignment using BLAST/BLIMPS (see the methods)
- Perform the prediction of mutation on the protein function using the protein alignment.

 
INSTALLATION:
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1- This script relies on a working installation of SIFT. Please install SIFT including Blast and Blimps as well as supporting databases (e.g. swiss.uni) before proceeding with this installation.
Please refer to SIFT help for this purpose (http://sift.jcvi.org/). See the following NOTE if you would like to use our version of these tools.

PLEASE NOTE THAT THE PROGRAM ASSUMES:
    - The BLAST executables reside in BLAST_DIR/bin/
    - The BLAST database resides in BLAST_DIR/db/swiss.uni
    - The program is tested using "Uniprot-TrEMBL" database. If you choose to use another database, please edit "align.pl" for the proper link to the database. The current script relies on "BLAST_DIR/db/swiss.uni". 

2- Copy all the perl scripts as well as the "config.txt" file in an arbitrary directory. 
3- Edit the existing config file (config.txt) with appropriate links to SIFT, BLAST, and BLIMPS. Please exactly follow the format as it is provided in the example.  

NOTE: A minimum version of SIFT, BLAST, and BLIMPS as well as supporting databases are available to download (indelz_supporting_applications.tar) from the website (http://www.moseslab.csb.utoronto.ca/amin/indelz.html).
Please follow these steps to make the tools ready:

> tar -xvf indelz_supporting_applications.tar
> tar -xvf sift4.0.3.tar.gz
> tar -xvf blimps-3.8.tar.gz
> tar -xvf blast-2.2.21.tar.gz
> tar -xvf blast-2.2.21.db.tar.gz

Now add links to these applications in the "config.txt" file. You are ready to use indelz. 

RUNNING THE SCRIPT:
-------------------

Running the script is simple (please use the exact order of inputs). 

>perl indelz.pl CONFIG_FILE INPUT_FASTA MUTATION_PATTERN

CONFIG_FILE: a text file with link to directories containing SIFT, BLAST, and BLIMPS. Also, the number of tries to make alignment using BLAST (default 10).
INPUT_FASTA: A text file with extension (.fasta or .fa) with the first line starting with ">" character followed by cDNA sequence of the protein of interest. 
MUTATION_PATTERN (seqeuence index begins from 1):

	> Nonsense mutation at DNA site 195:			195NM			(coordinate of mutated DNA base)
	> Premature Stop Codon at amino-acid residue 65: 	65Z			(coordinate of mutated amino-acid residue)
	> Deletion of 12 DNA bases at site 195:			195DEL(12)		
	> Insertion of "GCGCTGAC" at DNA site 195:		195INS(GCGCTGAC)	

Example:

> perl indelz.pl config.txt sample.fasta 195NM