Table of Contents

Computational Methods for Pseudogene Annotation Based on Sequence Homology.-  Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content.- Computational Methods of Identification of Pseudogenes Based on Functionality: Hybridization of 18S rRNA and mRNA During Translation.- Whole Genome Identification of Neutrally Evolving Pseudogenes Using the Evolutionary Measure dN/dS.- Methods to Study the Occurrence and the Evolution of Pseudogenes Through a Phylogenetic Approach.- Methods for Detecting Transcribed Pseudogenes: PCR on Regions of High Sequence Similarity Followed by Cloning and Sequencing,0 RNA Amplification for Pseudogene Detection Using RNA-Seq.- GENCODE Pseudogenes.- Methods to Detect Transcribed Pseudogenes: RNA-Seq Discovery Allows Learning Through Features.- Proteomics Techniques for the Detection of Translated Pseudogenes.- Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation.- Pseudogenes: A Novel Source of Trans Acting Antisense RNAs.- Pseudogene-Derived Endogenous siRNAs and Their Function.- Methods to Study Translated Pseudogenes: In Vitro Translation, Fusion with a Tag/Reporter Gene, and Complementation Assay.- Targeted and Robust Amplification of Mitochondrial DNA in the Presence of Nuclear Encoded Mitochondrial Pseudogenes Using Φ29 DNA Polymerases.- Discrimination of Pseudogene and Parental Gene DNA Methylation Using Allelic Bisulphite Sequencing Mutational Analysis of CYP21A2 Gene and CYP21A1P Pseudogene: Long Range PCR on Genomic DNA.- PMS2 Gene Mutational Analysis: RNA-Based Direct cDNA Sequencing to Circumvent Pseudogene Interference.- Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era.