ISDTool: A computational model for predicting immunosuppressive domain of HERVs

• Published in: Computational biology and chemistry Vol. 49; pp. 45 - 50
• Main Authors: Lv, Hongqiang, Han, Jiuqiang, Liu, Jun, Zheng, Jiguang, Zhong, Dexing, Liu, Ruiling
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.04.2014
• Subjects: Accuracy; Amino Acid Motifs; Amino Acid Sequence; Chromosomes, Human - virology; Computation; Computational Biology; Computer programs; Computer Simulation; Endogenous Retroviruses - chemistry; Endogenous Retroviruses - genetics; Endogenous Retroviruses - immunology; Evolutionary; Human; Human endogenous retrovirus; Humans; Immune Tolerance; Immunocompromised Host - immunology; Immunosuppressive domain prediction; ISDTool; Mathematical models; Molecular Sequence Data; Searching; Software; Terminal Repeat Sequences - genetics; Immunosuppressive domain prediction; Human endogenous retrovirus; ISDTool
• ISSN: 1476-9271; 1476-928X
• DOI: 10.1016/j.compbiolchem.2014.02.001

•A computational model for predicting ISD of HERVs is proposed.•1002 new putative ISDs of HERVs in the 24 human chromosomes have been predicted.•The model is also applicable to search for ISDs in HTLV, STLV and MLV.•Software named ISDTool has been developed. Human endogenous retroviruses (HERVs) have been found to act as etiological cofactors in several chronic diseases, including cancer, autoimmunity and neurological dysfunction. Immunosuppressive domain (ISD) is a conserved region of transmembrane protein (TM) in envelope gene (env) of retroviruses. In vitro and vivo, evidence has shown that retroviral TM is highly immunosuppressive and a synthetic peptide (CKS-17) that shows homology to ISD inhibits immune function. ISD is probably a potential pathogenic element in HERVs. However, only less than one hundred ISDs of HERVs have been annotated by researchers so far, and universal software for domain prediction could not achieve sufficient accuracy for specific ISD. In this paper, a computational model is proposed to identify ISD in HERVs based on genome sequences only. It has a classification accuracy of 97.9% using Jack-knife test. 117 HERVs families were scanned with the model, 1002 new putative ISDs have been predicted and annotated in the human chromosomes. This model is also applicable to search for ISDs in human T-lymphotropic virus (HTLV), simian T-lymphotropic virus (STLV) and murine leukemia virus (MLV) because of the evolutionary relationship between endogenous and exogenous retroviruses. Furthermore, software named ISDTool has been developed to facilitate the application of the model. Datasets and the software involved in the paper are all available at https://sourceforge.net/projects/isdtool/files/ISDTool-1.0.