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    BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins.

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    Author
    Selvaraj, M; Puri, M; Dikshit, KL; Lefevre, C
    Date
    2016
    Source Title
    Advances in Bioinformatics
    Publisher
    Hindawi Limited
    University of Melbourne Author/s
    Lefevre, Christophe
    Affiliation
    Medical Biology (W.E.H.I.)
    Metadata
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    Document Type
    Journal Article
    Citations
    Selvaraj, M., Puri, M., Dikshit, K. L. & Lefevre, C. (2016). BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins.. Adv Bioinformatics, 2016, pp.8150784-. https://doi.org/10.1155/2016/8150784.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/256182
    DOI
    10.1155/2016/8150784
    Open Access at PMC
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4789356
    Abstract
    The recent upsurge in microbial genome data has revealed that hemoglobin-like (HbL) proteins may be widely distributed among bacteria and that some organisms may carry more than one HbL encoding gene. However, the discovery of HbL proteins has been limited to a small number of bacteria only. This study describes the prediction of HbL proteins and their domain classification using a machine learning approach. Support vector machine (SVM) models were developed for predicting HbL proteins based upon amino acid composition (AC), dipeptide composition (DC), hybrid method (AC + DC), and position specific scoring matrix (PSSM). In addition, we introduce for the first time a new prediction method based on max to min amino acid residue (MM) profiles. The average accuracy, standard deviation (SD), false positive rate (FPR), confusion matrix, and receiver operating characteristic (ROC) were analyzed. We also compared the performance of our proposed models in homology detection databases. The performance of the different approaches was estimated using fivefold cross-validation techniques. Prediction accuracy was further investigated through confusion matrix and ROC curve analysis. All experimental results indicate that the proposed BacHbpred can be a perspective predictor for determination of HbL related proteins. BacHbpred, a web tool, has been developed for HbL prediction.

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