Application Note Systems Biology IMAN: Interlog protein network reconstruction, Matching and ANalysis Mohieddin Jafari 1,3* , Payman Nickchi 1 , Abdollah Safari 2 , Soheil Jahangiri Tazehkand 3 and Mehdi Mirzaie 4 1 Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, 69, Pasteur St, 13164, Tehran, Iran. 2 Department of Statistics and Actuarial Science, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, BC, Canada. 3 School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Shahid Lavasani St, PO Box 19395-5746, Tehran, Iran. 4 Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, PO Box 14115-134, Tehran, Iran. *Corresponding author: Tel: +98 21 6411 2466; Email: m_jafari@pasteur.ac.ir and mjafari@ipm.ir Associate Editor: XXXXXXX Received on XXXXX; revised on XXXXX; accepted on XXXXX Abstract Availability: IMAN package does not require any registration and is freely available at http://bs.ipm.ac.ir/softwares/IMAN or http://jafarilab-pasteur.com/content/software/IMAN.html. Contact: mjafari@ipm.ir Supplementary information: Supplementary data are available at Bioinformatics online. 1 Introduction Nowadays, technologies have provided access to tremendous amount of interactions at the molecular level. The study of these interactions, interactome, endeavor to model cellular and molecular events (1, 2). Among these interactions, protein-protein interactions (PPI) are signifi- cant due to functional and structural description of executive molecules i.e. proteins. However, PPI detection and prediction methods are still entangling with reducing false-positive and –negative interactions (3, 4). In addition to improvement of experimental and computational methods, data integration is the best solution overall. STRING (5), BioNetBuilder Cytoscape app (6), IMP 2.0 (7), PINALOG (8), HIPPIE (9) are using this solution to reconstruct and refine PPI networks (PPIN). Recently, an evolutionarily conserved network with communal nodes and less false- positive links, Interlog Protein Network (IPN), was introduced as a benchmark for the evaluation of clustering algorithms (10). IPN clears up the arisen and remained interactions during evolution and help to excavate the remnants of ancestor PPIN (10-14). In this study, we pro- vide a freely available R package to integrate several PPINs and retrieve IPNs. 2 Methods . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/069104 doi: bioRxiv preprint first posted online Aug. 11, 2016;