pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis

• Published in: BMC research notes 2009-10, Vol.2 (1), p.220-220
• Main Authors: Pellet, Johann, Meyniel, Laurène, Vidalain, Pierre-Olivier, de Chassey, Benoît, Tafforeau, Lionel, Lotteau, Vincent, Rabourdin-Combe, Chantal, Navratil, Vincent
• Format: Article
• Language: English
• Subjects: Biochemistry, Molecular Biology; Comparative analysis; Genomics; Life Sciences; Nucleotide sequence; Protein-protein interactions; Technical Note; Two-hybrid system
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/1756-0500-2-220

High-throughput screening of protein-protein interactions opens new systems biology perspectives for the comprehensive understanding of cell physiology in normal and pathological conditions. In this context, yeast two-hybrid system appears as a promising approach to efficiently reconstruct protein interaction networks at the proteome-wide scale. This protein interaction screening method generates a large amount of raw sequence data, i.e. the ISTs (Interaction Sequence Tags), which urgently need appropriate tools for their systematic and standardised analysis. We develop pISTil, a bioinformatics pipeline combined with a user-friendly web-interface: (i) to establish a standardised system to analyse and to annotate ISTs generated by two-hybrid technologies with high performance and flexibility and (ii) to provide high-quality protein-protein interaction datasets for systems-level approach. This pipeline has been validated on a large dataset comprising more than 11.000 ISTs. As a case study, a detailed analysis of ISTs obtained from yeast two-hybrid screens of Hepatitis C Virus proteins against human cDNA libraries is also provided. We have developed pISTil, an open source pipeline made of a collection of several applications governed by a Perl script. The pISTil pipeline is intended to laboratories, with IT-expertise in system administration, scripting and database management, willing to automatically process large amount of ISTs data for accurate reconstruction of protein interaction networks in a systems biology perspective. pISTil is publicly available for download at http://sourceforge.net/projects/pistil.