MultiP 0.5 - A Program for Predicting Chloroplast Proteins

By Jong Kyoung Kim


Version 0.5 released on May 24, 2008

Introduction

MultiP 0.5 is a suite of programs for predicting chloroplast localization of plant proteins, based on the N-terminal transit peptide sequences. It consists of three independent programs for

1 Motif Search:   searching motifs which were experimentally verified in the paper

2 Motif Discovery:   identifying novel motifs

3 Chloroplast Localization Prediction:   predicting chloroplast transit peptides

The all programs are implemented completely in MATLAB. The required version of MATLAB is 7.3 or higher including Bioinformatics Toolbox.


Motif Search

The program motif_search determines whether an input sequence has the motifs of RbcS, BCCP, Cab, DnaJ-J8, PORA, TOCC, and GLU2 by calculating the p-values of the scores of global alignments with dual gap penalties. For search, 80 amino acids residues of the N-terminal regions are used.


Motif Discovery

The program motif_discovery takes a query sequence as input and predicts putative sequence motifs. The predicted motifs is an ordered set of sequence motifs that maximally discriminate between the positive (the sequences from plastid transit peptides) and the negative (the N-termini of non-plastid proteins) sets. For discovery, 80 amino acids residues of the N-terminal regions should be used.


Chloroplast Localization Prediction

The program chloroplast_loc_prediction takes a query sequence as input and predicts whether it is targeted to chloroplast or not. For prediction, 60 amino acids residues of the N-terminal regions are used.


Installation

On Windows systems, download the zip file and extract it. It will make a folder called MultiP. Then, run MATLAB and change the current directory into MultiP. To use the program chloroplast_loc_prediction, LIBSVM should be installed. After installing LIBSVM, add the directory for LIBSVM to the search path of MATLAB (File->Set Path->Add Folder->Save).


Download

The current release (Version 0.5, May 24, 2008) of MultiP can be obtained by downloading the zip file. [ MultiP Download ]

To use the program chloroplast_loc_prediction, LIBSVM should be properly installed. LIBSVM can be downloaded from [ LIBSVM Download ] or the LIBSVM webpage.


Citation