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

doi:10.1186/1756-0500-2-220

BMC Research Notes

Volume 2

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Pellet J
Meyniel L
Vidalain PO
de Chassey B
Tafforeau L
Lotteau V
Rabourdin-Combe C
Navratil V

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Pellet J
Meyniel L
Vidalain PO
de Chassey B
Tafforeau L
Lotteau V
Rabourdin-Combe C
Navratil V
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Technical Note

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

Johann Pellet¹^,2^,3 , Laurène Meyniel¹^,2^,3 , Pierre-Olivier Vidalain⁴ , Benoît de Chassey¹^,2^,3 , Lionel Tafforeau¹^,2^,3 , Vincent Lotteau¹^,2^,3 , Chantal Rabourdin-Combe¹^,2^,3^* and Vincent Navratil¹^,2^,3^,5^,6^*

¹U851, INSERM, 21 avenue Tony Garnier, F-69007, Lyon, France

²Université de Lyon, Lyon, France

³IFR128, Université Lyon 1, Lyon, France

⁴Laboratoire de Génomique Virale et Vaccination, Institut Pasteur, CNRS, URA 3015, Paris, France

⁵UMR754, INRA, ENVL, Lyon, France

⁶Current address: Centre de RMN à Très Hauts Champs, CNRS, 5 rue de la Doua, 69100, Villeurbanne, France

author email corresponding author email* Contributed equally

BMC Research Notes 2009, 2:220doi:10.1186/1756-0500-2-220


Published:	29 October 2009

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.

Findings

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.

Conclusion

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 webcite.