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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto

Viswanadham Sridhara1, Aron Marchler-Bauer, Stephen H Bryant

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD, USA.

Database : the Journal of Biological Databases and Curation
|May 17, 2011
PubMed
Summary

This study identifies evolutionarily conserved protein phosphorylation sites across human, mouse, and fruit fly genomes. This comparative genomics approach enables accurate prediction of thousands of new phosphorylation sites, advancing functional genomics research.

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Next-generation sequencing has increased complete genome data.
  • Functional characterization of genomes via high-throughput proteomics is challenging due to scalability issues.
  • Comparative genomics can transfer experimental results between species, minimizing errors.

Purpose of the Study:

  • To leverage comparative genomics for functional characterization of protein phosphorylation sites.
  • To identify evolutionarily conserved phosphorylation sites across multiple species.
  • To scale phosphosite annotation using conserved domains.

Main Methods:

  • Utilized large-scale phosphoproteomics data from Homo sapiens, Mus musculus, and Drosophila melanogaster.
  • Mapped phosphorylation sites onto conserved domains in NCBI's Conserved Domain Database (CDD).
  • Transferred phosphorylation annotations to homologous proteins sharing conserved domains.

Main Results:

  • Identified 25 evolutionarily conserved phosphorylation sites among the three species.
  • Generated 3253 phosphosite annotations for coelomata proteins based on conserved domains.
  • Demonstrated a scalable method for phosphosite discovery.

Conclusions:

  • Comparative genomics is effective for identifying conserved functional elements like phosphorylation sites.
  • This method significantly expands the annotation of phosphosites in proteomes.
  • The approach is highly scalable with increasing phosphoproteomics data.