Protein Sequence Comparison and DNA-binding Protein Identification with Generalized PseAAC and Graphical Representation

Li, Chun; Zhao, Jialing; Wang, Changzhong; Yao, Yuhua

DNA-binding proteins (DNA-BPs) are very important functional proteins in a cell. These proteins play vital roles in various cellular processes, including DNA replication, transcription, regulation of gene expression, packaging, and other activities associated with DNA [1] [2] [3] [4] [5] . It is therefore substantially important to distinguish DNA-BPs from non-DNA-binding proteins (NBPs). In the past, many experimental and computational techniques have been developed for identifying DNA-BPs. Experimental techniques can provide a clear-cut answer to a query protein. However, the experimental methods are cost-intensive and time-consuming, and thus impractical for large datasets [3] [4] [5] [6] [7] . Computational methods can be broadly divided into two categories: structure-based method and sequence-based *Address correspondence to this author at the School of Mathematics and Statistics, Hainan Normal University, Haikou 571158, China; Tel: [phone]; E-mail: [e-mail] method. The former can discriminate DNA-binding and nonbinding proteins with high accuracy, but these methods can't be employed in high throughput annotation, as they require the structure information of a query protein [1] . Though tremendous progress has been achieved in experimental determination of protein structures in the past five decades, it can't keep pace with the explosive growth of sequence information resulting from modern sequencing technology [8] . Yet as suggested by Anfinsen [9] , proteins contain within their amino acid sequences enough information to determine their native conformation. Therefore, it is more promising to use sequence-based methods to identify DNA-BPs.