title: pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: U851, INSERM, 21 avenue Tony Garnier, F-69007, Lyon, France. johann.pellet@inserm.fr
authors.forename: Johann
authors.initials: J
authors.lastname: Pellet
authors.forename: Laurène
authors.initials: L
authors.lastname: Meyniel
authors.forename: Pierre-Olivier
authors.initials: PO
authors.lastname: Vidalain
authors.forename: Benoît
authors.initials: B
authors.lastname: de Chassey
authors.forename: Lionel
authors.initials: L
authors.lastname: Tafforeau
authors.forename: Vincent
authors.initials: V
authors.lastname: Lotteau
authors.forename: Chantal
authors.initials: C
authors.lastname: Rabourdin-Combe
authors.forename: Vincent
authors.initials: V
authors.lastname: Navratil