Background: Subcellular localization prediction of protein is an important component of bioinformatics, which has great importance for drug design and other applications. A multitude of computational tools for proteins subcellular location have been developed in the recent decades, however, existing methods differ in the protein sequence representation techniques and classification algorithms adopted.
Results: In this paper, we firstly introduce two kinds of protein sequences encoding schemes: dipeptide information with space and Gapped k-mer information. Then, the Gapped k-mer calculation method which is based on quad-tree is also introduced.
Conclusions: >From the prediction results, this method not only reduces the dimension, but also improves the prediction precision of protein subcellular localization.
Keywords: Gene ontology; Physicochemical properties; Position-specific score matrix; Principal component analysis; Support vector machine.