Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs.
BACKGROUND
The subcellular location of a protein is closely correlated to its function. Thus, computational prediction of subcellular locations from the amino acid sequence information would help annotation and functional prediction of protein coding genes in complete genomes. We have developed a method based on support vector machines (SVMs).


RESULTS
We considered 12 subcellular locations in eukaryotic cells: chloroplast, cytoplasm, cytoskeleton, endoplasmic reticulum, extracellular medium, Golgi apparatus, lysosome, mitochondrion, nucleus, peroxisome, plasma membrane, and vacuole. We constructed a data set of proteins with known locations from the SWISS-PROT database. A set of SVMs was trained to predict the subcellular location of a given protein based on its amino acid, amino acid pair, and gapped amino acid pair compositions. The predictors based on these different compositions were then combined using a voting scheme. Results obtained through 5-fold cross-validation tests showed an improvement in prediction accuracy over the algorithm based on the amino acid composition only. This prediction method is available via the Internet.
Park
Keun-Joon
KJ
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
Kanehisa
Minoru
M
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism; D001185:Artificial Intelligence; D022082:Cellular Structures / Q000737:chemistry / Q000378:metabolism; D003205:Computing Methodologies; D030562:Databases, Protein; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013347:Subcellular Fractions / Q000737:chemistry* / Q000378:metabolism*; D014018:Tissue Distribution
D000596:Amino Acids; D011506:Proteins