BacHbpred: Support vector machine methods for the prediction of bacterial hemoglobin-like proteins

MuthuKrishnana Selvaraj, Munish Puri, Kanak Dikshit, Christophe Lefevre

    Research output: Contribution to journalArticle

    3 Citations (Scopus)

    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.

    Original languageEnglish
    Article number8150784
    Pages (from-to)Art: 8150784
    Number of pages12
    JournalAdvances in Bioinformatics
    Volume2016
    DOIs
    Publication statusPublished - 1 Jan 2016

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