DarkHorse HGT Candidate Resource
A database of phylogenetically atypical microbial proteins
Program Description: Darkhorse is an experimental program that defines phylogenetic relatedness of BLASTP hits for a set of proteins against the NCBI Genbank nr database, using a lineage probability index (LPI) score. The basic algorithm used to calculate LPI scores and its application in predicting horizontal gene transfer are described in the following publications:
Hardware requirements: A multi-processor CPU with clock speed of at least 1.0 GHz is recommended. There must be sufficient hard disk space available to store the entire GenBank nr sequence database, (currently 12 Gb) plus several large MySQL tables based on this database. Total disk space required is roughly double the size of the Genbank nr database. This requirement will expand proportionally as new sequences are added to Genbank. Program performance depends primarily on MySQL database access efficiency.
Software requirements: DarkHorse requires the Unix OS. It has been installed, tested, and run successfully on Sun Solaris (v. 9), Apple Macintosh (OS X 10.4), and Linux (RedHat Enterprise v. 4) platforms. It cannot be run using Microsoft Windows. The following additional third-party software must be pre-installed:
Prior to DarkHorse program installation, a database must be created from within the MySQL program to accept DarkHorse input, e.g.
mysql> create database darkhorse_01;
The following public database information must be downloaded, de-compressed, and locally available:
Users must be able to obtain protein BLAST search data for query sequences versus the Genbank nr database, with output in the NCBI -m8 (tab-delimited) format. Alternative BLAST engines (e.g. cluster accelerated) can be used instead of the NCBI version, as long as the output ends up in the same tab-delimited format. These tab-delimited output files are used as DarkHorse program input.
The stand-alone software is provided as a unix archive, which must be decompressed and extracted before use:tar -xzvf DarkHorse-1.4_rev163.tar.gz
Instructions for installation and use are provided in a README.txt file, which may be downloaded separately below.
Version 1.4 July 19, 2010
Version 1.3 December 14, 2009
Version 1.2 August 19, 2009
Version 1.1 April 6, 2009
Version 1.0 October 24, 2008
Version 0.9 May 9, 2008
Version 0.8 August 15, 2007