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JFeature: A Java Package for Extracting Global Sequence Features from Proteins for Functional Classification
Abstract
Prediction of various functional properties of proteins has long been a central theme of bioinformatics in the post-genomic era. Statistical learning, in addition to analysis based on sequence similarity, was proven successful to detect complex sequence-function associations in many applications. JFeature is an integrated Java tool to facilitate extraction of global sequence features and preparation of example sets, in statistical learning studies of sequence-function relationships. With a user-friendly graphical interface, it computes the composition, distribution, transition and auto-correlation features from sequence. It also helps to assemble a negative example set based on the most-dissimilar principle. The Java package and supplementary documentations are available at http://www.cls.zju.edu.cn/rlibs/software/jfeature.html.
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