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Pseudogenes

Overview of attention for book
Cover of 'Pseudogenes'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Pseudogene Redux with New Biological Significance
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    Chapter 2 Contribution of Pseudogenes to Sequence Diversity
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    Chapter 3 Computational Methods for Pseudogene Annotation Based on Sequence Homology
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    Chapter 4 Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content.
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    Chapter 5 Methods of Identification of Pseudogenes Based on Functionality: Hybridization of 18S rRNA and mRNA During Translation
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    Chapter 6 Whole-Genome Identification of Neutrally Evolving Pseudogenes Using the Evolutionary Measure dN/dS
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    Chapter 7 Methods to study the occurrence and the evolution of pseudogenes through a phylogenetic approach.
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    Chapter 8 Methods for Detecting Transcribed Pseudogenes: PCR on Regions of High Sequence Similarity Followed by Cloning and Sequencing
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    Chapter 9 RNA Amplification for Pseudogene Detection Using RNA-Seq.
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    Chapter 10 GENCODE Pseudogenes
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    Chapter 11 Methods to Detect Transcribed Pseudogenes: RNA-Seq Discovery Allows Learning Through Features
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    Chapter 12 Proteomics techniques for the detection of translated pseudogenes.
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    Chapter 13 Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation.
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    Chapter 14 Pseudogenes: A Novel Source of trans-Acting Antisense RNAs
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    Chapter 15 Pseudogene-Derived Endogenous siRNAs and Their Function
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    Chapter 16 Methods to Study Translated Pseudogenes: In Vitro Translation, Fusion with a Tag/Reporter Gene, and Complementation Assay
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    Chapter 17 Targeted and robust amplification of mitochondrial DNA in the presence of nuclear-encoded mitochondrial pseudogenes using φ29 DNA polymerases.
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    Chapter 18 Pseudogenes
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    Chapter 19 Mutational Analysis of CYP21A2 Gene and CYP21A1P Pseudogene: Long-range PCR on Genomic DNA.
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    Chapter 20 PMS2 Gene Mutational Analysis: Direct cDNA Sequencing to Circumvent Pseudogene Interference
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    Chapter 21 Dealing with Pseudogenes in Molecular Diagnostics in the Next-Generation Sequencing Era
Attention for Chapter 4: Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content.
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Chapter title
Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content.
Chapter number 4
Book title
Pseudogenes
Published in
Methods in molecular biology, April 2014
DOI 10.1007/978-1-4939-0835-6_4
Pubmed ID
24823770
Book ISBNs
978-1-4939-0834-9, 978-1-4939-0835-6
Authors

Evgeniy S Balakirev, Vladimir R Chechetkin, Vasily V Lobzin, Francisco J Ayala, Evgeniy S. Balakirev Ph.D., Vladimir R. Chechetkin, Vasily V. Lobzin, Francisco J. Ayala, Evgeniy S. Balakirev

Editors

Laura Poliseno

Abstract

Spectral entropy and GC content analyses reveal comprehensive structural features of DNA sequences. To illustrate the significance of these features, we analyze the β-esterase gene cluster, including the Est-6 gene and the ψEst-6 putative pseudogene, in seven species of the Drosophila melanogaster subgroup. The spectral entropies show distinctly lower structural ordering for ψEst-6 than for Est-6 in all species studied. However, entropy accumulation is not a completely random process for either gene and it shows to be nucleotide dependent. Furthermore, GC content in synonymous positions is uniformly higher in Est-6 than in ψEst-6, in agreement with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of ψEst-6 and Est-6 after the duplication event. The data obtained show the relevance and significance of entropy and GC content analyses for pseudogene identification and for the comparative study of gene-pseudogene evolution.

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X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
 Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 14 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Netherlands 1 7%
Unknown 13 93%

Demographic breakdown

Readers by professional status Count As %
Professor 4 29%
Researcher 2 14%
Student > Ph. D. Student 2 14%
Student > Bachelor 1 7%
Librarian 1 7%
Other 2 14%
Unknown 2 14%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 7 50%
Neuroscience 2 14%
Agricultural and Biological Sciences 2 14%
Computer Science 1 7%
Unknown 2 14%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 November 2019.
All research outputs
#15,330,390
of 23,577,654 outputs
Outputs from Methods in molecular biology
#4,903
of 13,410 outputs
Outputs of similar age
#130,007
of 228,568 outputs
Outputs of similar age from Methods in molecular biology
#32
of 136 outputs
Altmetric has tracked 23,577,654 research outputs across all sources so far. This one is in the 32nd percentile – i.e., 32% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,410 research outputs from this source. They receive a mean Attention Score of 3.4. This one has gotten more attention than average, scoring higher than 58% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 228,568 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 40th percentile – i.e., 40% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 136 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 75% of its contemporaries.

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