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Open Access Software

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data

Kuo Ping Chiu1, Chee-Hong Wong2, Qiongyu Chen3, Pramila Ariyaratne1, Hong Sain Ooi1, Chia-Lin Wei4, Wing-Kin Ken Sung13 and Yijun Ruan4*

Author Affiliations

1 Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome #02-01, 138672, Singapore

2 Bioinformatics Institute, 30 Biopolis Street, Matrix #08-01, 138671, Singapore

3 Department of Computer Science, National University of Singapore, 3 Science Drive 2, 117543, Singapore

4 Genome Technology and Biology Group, Genome Institute of Singapore, 60 Biopolis Street, Genome #02-01, 138672, Singapore

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BMC Bioinformatics 2006, 7:390  doi:10.1186/1471-2105-7-390

Published: 25 August 2006



We recently developed the Paired End diTag (PET) strategy for efficient characterization of mammalian transcriptomes and genomes. The paired end nature of short PET sequences derived from long DNA fragments raised a new set of bioinformatics challenges, including how to extract PETs from raw sequence reads, and correctly yet efficiently map PETs to reference genome sequences. To accommodate and streamline data analysis of the large volume PET sequences generated from each PET experiment, an automated PET data process pipeline is desirable.


We designed an integrated computation program package, PET-Tool, to automatically process PET sequences and map them to the genome sequences. The Tool was implemented as a web-based application composed of four modules: the Extractor module for PET extraction; the Examiner module for analytic evaluation of PET sequence quality; the Mapper module for locating PET sequences in the genome sequences; and the ProjectManager module for data organization. The performance of PET-Tool was evaluated through the analyses of 2.7 million PET sequences. It was demonstrated that PET-Tool is accurate and efficient in extracting PET sequences and removing artifacts from large volume dataset. Using optimized mapping criteria, over 70% of quality PET sequences were mapped specifically to the genome sequences. With a 2.4 GHz LINUX machine, it takes approximately six hours to process one million PETs from extraction to mapping.


The speed, accuracy, and comprehensiveness have proved that PET-Tool is an important and useful component in PET experiments, and can be extended to accommodate other related analyses of paired-end sequences. The Tool also provides user-friendly functions for data quality check and system for multi-layer data management.