(a)Theconceptofpairendditag(PET)analysisPaired.pptVIP

(a) The concept of pair end ditag (PET) analysis. Paired tags from both 5￠ and 3￠ ends of the DNA molecule are simultaneously extracted and covalently linked as a unit. Upon sequencing and mapping analysis, the mapping coordinates on the reference genome define the identity of target DNA and its location. (b) Methods to generate PET sequencing templates. Adaptor containing type IIs restriction enzyme is added to each end of DNA. The adapter-ligated DNA ends are either connected by cloning vector or self-circularized followed by enzymatic digestion to release the PETs. Depending on the enzymes used, the tag length can be varied from 20 to 27 bp. (c) PET sequencing strategy. PET structures can be sequenced by all the commercially available sequencing platforms. PET can be concatenated as 10–20 units for capillary electrophoresis (CE) sequencing, 2–4 units for pyrosequencing or directly used as single unit in the pair-end-tag sequencing protocol by GA or SOLiD. Y Ruan et al. WIREs Syst Biol Med 2010. DOI: 10.1002/wsbm.040 Copyright ? 2009 John Wiley Sons, Inc. Gene Identification Signature by Pair End diTag (GIS-PET) analysis for gene identification and genome annotation. (a) PET is extracted from full length cDNA and mapped to reference genome. The mapping coordinates can demarcate the boundaries of expressed full length transcripts, define transcriptional units, and annotate genome for new genes and promoters. (b) An example of GIS-PET structure and its location on chr.1:148040294–148053009. The numbers on the left represent the frequency of this cluster of PETs annotated to PSMD4 gene and tracks below show the same genes represented by Transfrag, transcription associated regions (TARs), cap analysis of gene expression (CAGE) and promoter assays. Y Ruan et al. WIREs Syst Biol Med 2010. DOI: 10.1002/wsbm.040 Copyright ? 2009 John Wiley Sons, Inc. Structure variations detected by g-PET analysis. (a) Genomic DNA of specific sizes (2, 5, or 10 Kb) is selected and sel