Software - Protein Homology Detection Through Alignment of Markov Random Fields - page 31

Chapter 3
Software

Abstract This chapter introduces the software implementing the ideas presented in
the Method chapter. It covers installation, usage and result interpretation of the
software.

Keywords MRFalign MRFsearch P-value

MRFpred is a protein homology detection program that implements the above-
described method. It is freely available at http://raptorx.uchicago.edu/download/ .

3.1 Overview of Program

The MRFpred package (X86_64 Linux version with OpenMPI installed) consists of
the following three main programs:

buildFeature Generating features for a given protein sequence.
MRFalign Aligning two protein sequences by aligning their corresponding

MRFs. The program will take two protein feature files as input and

output their alignment and some details such as alignment score.

MRFsearch Searching a given protein database for a query protein sequence to

find its homologs. This program uses MRFalign to build alignments
and then rank all the proteins in the database by alignment score.

You can simply run a program without arguments to obtain the help information.

3.2 Software Download

The whole MRFpred package includes the following files,

1. MRFsearch_v1.1.tar.gz ( 100M): the package contains all the programs.

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2. TGT_BC40.tar.gz ( 900M): a protein database for homology search, in which

any two proteins share <40 % sequence identity.

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