Prediction of lysine formylation sites using the composition of k-spaced amino acid pairs via Chou's 5-steps rule and general pseudo components

Lysine formylation is a newly discovered post-translational modification in histones, which plays a crucial role in epigenetics of chromatin function and DNA binding. In this study, a novel bioinformatics tool named CKSAAP_FormSite is proposed to predict lysine formylation sites. An effective feature extraction method, the composition of k-spaced amino acid pairs, is employed to encode formylation sites. Moreover, a biased support vector machine algorithm is proposed to solve the class imbalance problem in the prediction of formylation sites. As illustrated by 10-fold cross-validation, CKSAAP_FormSite achieves an satisfactory performance with an AUC of 0.8234. Therefore, CKSAAP_FormSite can be a useful bioinformatics tool for the prediction of formylation sites. Feature analysis shows that some amino acid pairs, such as ‘KA’, ‘SxxxxK’ and ‘SxxxA’ around formylation sites may play an important role in the prediction. The results of analysis and prediction could offer useful information for elucidating the molecular mechanisms of formylation.