pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysisReport as inadecuate




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BMC Research Notes

, 2:220

First Online: 29 October 2009Received: 15 June 2009Accepted: 29 October 2009DOI: 10.1186-1756-0500-2-220

Cite this article as: Pellet, J., Meyniel, L., Vidalain, PO. et al. BMC Res Notes 2009 2: 220. doi:10.1186-1756-0500-2-220

Abstract

BackgroundHigh-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.

FindingsWe 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.

ConclusionWe 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.

Abbreviationsbpbase pairs

ESTExpressed Sequence Tag

ISTInteraction Sequence Tag

ntnucleotide

PSI-MIProteomics Standards Initiative-Molecular Interaction

Y2HYeast Two-Hybrid

ABIApplied Biosystems INC

SCFStandard Chromatogram Format

HTMLHypertext Markup Language.

Chantal Rabourdin-Combe and Vincent Navratil contributed equally to this work.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-2-220 contains supplementary material, which is available to authorized users.

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Author: Johann Pellet - Laurène Meyniel - Pierre-Olivier Vidalain - Benoît de Chassey - Lionel Tafforeau - Vincent Lotteau - Chant

Source: https://link.springer.com/







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