README SOFTWARE NAME: SNPidentifier
VERSION: beta 1.10, February 2009
AUTHORS: Danielle Gorbach, Zhi-Liang Hu, and Max Rothschild
BRIEF DESCRIPTION:
This package is designed to predict the location of SNPs from clusters
of ESTs produced by the program CAP3. For more details, please refer
to the documentation that is distributed together with the package.
PUBLICATION:
Gorbach, Danielle M., Zhi-Liang Hu, Zhi-Qiang Du and M. F. Rothschild (2009)
"SNP discovery in Litopenaeus vannamei with a new computational pipeline".
Animal Genetics, 40(1):106-109.
PLATFORM and ENVIRONMENT REQUIREMENT:
Dos, Windows 3.x, 9x, 2000, NT, XP, Linux, Unix, and any other platform
where perl 5.8.0 or above and required libraries are installed
DOWNLOAD:
http://www.animalgenome.org/bioinfo/tools/share/SNPidentifier/script.tar.gz
INSTALLATION:
* On Linux/Unix/Mac OS X platforms:
1. Download and unpackage the program ('gunzip', 'tar -xf-'; or 'tar zxf');
2. Change the first line in the program with proper path pointing to perl
in your system;
3. Make the program file excutable (e.g. on unix/Linux, do "chmod 755").
* On Windows platforms:
The steps are similar; except that you need to install ActivePerl to run it.
Although you can make it a ".exe" file but it's recommanded to run on command
line. You may need UnZip or RAR to uncompress the downloaded file.
USAGE:
To run this program, follow these steps:
1) Change the first line of this program to point to the correct path
for perl on your computer.
2) Perl 5.8.0 or higher (ActivePerl for Windows machine) much be installed
on your computer.
3) You must have a set of contigs that were obtained from CAP3 run of
your raw sequences (the CAP3 alignment serves as your input file).
4) Run this program on command line (For Windows, open the command prompt;
For Mac OS or Linux, bring up the terminal window): change directory
to the location of this program. Then type the name of the program and
hit "enter" to run.
> script_name
DATA INPUT:
This program takes standard output (displaying consensus sequence
alignments) from "cap3" as input. No modification is needed.
DATA OUTPUT:
This program outputs results in two files:
- One file (default name "find.snp.seq.txt") contains all consensus
sequences that are identified to contain at least one SNP. Each record
is tab delimited:
1. Name of the sequence
2. Sequence itself
- One file (default name "find.snp.sta.txt") contains all statistics
that descibe each virtually identified SNP. The statistics are tab-
delimited, one line for each SNP, include:
1. SNP scores (minor allele frequency x the number of sequences
containing the minor allele).
2. The contig number (sequence name)
3. SNP location (number of bases from left end of the seq.)
4. Minor nucleotide (allele) frequencies
5. Number of aligned sequences that contribute to the SNP scoring
WEB SITE:
Check the SNPidentifier web site for recent changes and future updates:
http://www.animalgenome.org/bioinfo/tools/share/SNPidentifier/
AUTHOR'S CLAIM:
This is a trial version which we authorize for non-profit use and
distribution for evaluation. We are not responsible for possible
errors that may exist in the program. Any use of the package is free
provided that the purpose of use is for evaluation, education and non-
profit research. The authors appreciate feedbacks from users for further
improvement. Original codes are available upon request to the authors.
All other rights are reserved that include modification and recompilation
of the programs.
REFERENCE:
Gorbach DM, Hu ZL, Du ZQ, Rothschild MF. (2009).
SNP discovery in Litopenaeus vannamei with a new computational pipeline.
Anim Genet. Volume 40, Issue 1, pages 106-109.
CONTACT:
For any question using the software or suggestions to improve, contact:
zhu iastate.edu
mfrothsciastate.edu
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Documentation 
script.tar.gz 
