Abstract
BackgroundWe 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.ResultsWe 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.ConclusionThe 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.
Highlights
We recently developed the Paired End diTag (PET) strategy for efficient characterization of mammalian transcriptomes and genomes
PET-based DNA analyses (GIS-PET and chromatin immunoprecipitation (ChIP)-PET) promise to play a significant role in the post-genome efforts to identify all functional elements in the human genome [11], and there is no inherent limit for the PET-based approach to be applied to other DNA analyses, such as analyses of epigenetic elements
There is a battery of new bioinformatics challenges around how to accurately identify and extract PET sequences embedded in raw sequence reads, how to and efficiently map the paired 5' and 3' signatures of PET sequences in complex genomes such as the human and mouse genome sequences; and how to be user-friendly in managing the immense amount of data generated from Gene Identification Signature (GIS)-PET and ChIP-PET experiments for effective data mining and analysis
Summary
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. Over 70% of quality PET sequences were mapped 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
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