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Related Concept Videos

Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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Related Experiment Video

Updated: Jun 28, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Pseudofam: the pseudogene families database.

Hugo Y K Lam1, Ekta Khurana, Gang Fang

  • 1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

Nucleic Acids Research
|October 30, 2008
PubMed
Summary
This summary is machine-generated.

Pseudofam is a database of pseudogene families, offering tools to analyze pseudogene structure and evolution. It reveals that housekeeping gene families often contain numerous pseudogenes, suggesting significant evolutionary activity.

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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Related Experiment Videos

Last Updated: Jun 28, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Pseudogenes, non-functional gene relics, play roles in gene regulation and evolution.
  • Understanding pseudogene families aids in deciphering evolutionary processes and genomic complexity.

Purpose of the Study:

  • To introduce Pseudofam, a comprehensive database for pseudogene family analysis.
  • To provide resources for investigating pseudogene origins, evolution, and genomic associations.

Main Methods:

  • Utilized a large-scale parallelized homology search algorithm (PseudoPipe extension) for pseudogene identification.
  • Integrated Pfam domain alignments to classify pseudogenes into protein families.
  • Developed an ontology for annotating pseudogene creation, history, and genomic context.

Main Results:

  • Pseudofam version 1.0 contains over 125,000 pseudogenes from 10 eukaryotic genomes, organized into nearly 3000 families.
  • Identified associations between pseudogene families and genomic features like segmental duplications.
  • Statistical analysis revealed housekeeping families are enriched with pseudogenes, and correlated gene/pseudogene counts across species.

Conclusions:

  • Pseudofam provides a valuable resource for pseudogene research, facilitating large-scale analysis.
  • Pseudogene family analysis offers insights into evolutionary dynamics and the prevalence of pseudogenization in specific gene categories.
  • The database highlights the significant role of pseudogenes in evolutionary processes and genomic evolution.