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BioSeq-Analysis is a platform for DNA, RNA, and protein sequence analysis based on machine learning approaches |
Because of its importance, recently some web-servers or stand-alone tools have been developed to facilitate the developments of the biological sequence analysis field, for example, repDNA [1], PseKNC [2], PseKNC-General [3], RepRNA [4] were constructed to generate the features of DNA/RNA sequences, and PseAAC [5], Propy [6] were designed to extract the features of protein sequences. Recently, the Pse-in-One [7, 8] has been established to generate and analyze the features of DNA, RNA, and protein sequences with the properties defined by users themselves according to their requirements. The Pse-Analysis [9] made a further attempt to construct an intelligent system by incorporating the feature extraction algorithms into Support Vector Machines.
All these aforementioned tools and web-servers have been widely used in the field of biological sequence analysis, and have played a role in simulating the development of this very important field. However, further work is needed due to the following reasons: (1) Although some tools have been proposed for establishing the biological sequence analysis predictors, they only focus on specific individual step. An automatically platform is required to promote the development of the computational predictors in this field; (2) It is never an easy task to find the optimized features, classifiers, and their combinations when establishing a predictor for biological sequence analysis; (3) All the available tools have missed some features or machine learning classifiers proposed very recently.
The present study was initiated an attempted to overcome the three shortcomings by establishing a powerful platform for biological sequence analysis based on machine learning techniques called BioSeq-Analysis. It combines the three main processes including feature extraction, predictor construction, and performance evaluation. All the parameters in the three steps can be automatically optimized. It is anticipated that BioSeq-Analysis would be a powerful tool in biological sequence analysis.
REFERENCES
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