title: BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins.
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.
authors.affiliation: Institute of Microbial Technology (CSIR), Sector 39A, Chandigarh 160036, India; Fermentation and Protein Biotechnology Laboratory, Department of Biotechnology, Punjabi University, Patiala 147002, India.
authors.forename: MuthuKrishnan
authors.initials: M
authors.lastname: Selvaraj
authors.affiliation: Fermentation and Protein Biotechnology Laboratory, Department of Biotechnology, Punjabi University, Patiala 147002, India; Centre for Chemistry and Biotechnology, Deakin University, Geelong, VIC 3217, Australia.
authors.forename: Munish
authors.initials: M
authors.lastname: Puri
authors.affiliation: Institute of Microbial Technology (CSIR), Sector 39A, Chandigarh 160036, India.
authors.forename: Kanak L
authors.initials: KL
authors.lastname: Dikshit
authors.affiliation: Centre for Chemistry and Biotechnology, Deakin University, Geelong, VIC 3217, Australia.
authors.forename: Christophe
authors.initials: C
authors.lastname: Lefevre