MultiP 0.5 - A Program for Predicting Chloroplast Proteins
By Jong Kyoung Kim
Version 0.5 released on May 24, 2008
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
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.
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.
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.
- Load a file in FASTA format for a single sequence or several sequences.
>>S = fastaread('input.txt');
- Run the program chloroplast_loc_prediction. For example, if the input file to search motifs is input.txt
and the output file to write results is output.txt
>>[pred_label, prob] = chloroplast_loc_prediction(S,'output.txt');
- The outputs pred_label and prob correspond to predicted labels (1: chloroplast, 2: non-chloroplast) and their prediction probabilities, respectively.
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).
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.