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Related Concept Videos

Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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...
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.
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Target selection for structural genomics: a single genome approach.

Igor V Grigoriev1, In-Geol Choi

  • 1Department of Chemistry and E.O. Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, USA. igor-grigoriev@sugen.com

Omics : a Journal of Integrative Biology
|March 11, 2003
PubMed
Summary
This summary is machine-generated.

Structural genomics of Mycoplasma identified few easy protein targets. Challenges include codon bias, membrane proteins, and large domains, necessitating novel approaches for difficult targets.

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Area of Science:

  • Structural biology
  • Genomics
  • Microbiology

Background:

  • Structural genomics aims to determine protein structures for a whole genome.
  • Studying microbial genomes like Mycoplasma genitalium and Mycoplasma pneumoniae provides insights into target selection strategies.

Purpose of the Study:

  • To outline a strategy for selecting protein structure determination targets within a single genome context.
  • To identify challenges and reasons for the scarcity of easily targetable genes for high-throughput structural studies.

Main Methods:

  • Analysis of Mycoplasma genitalium and Mycoplasma pneumoniae genomes for target selection.
  • Evaluation of criteria including protein fold prediction, expression in E. coli, and protein characteristics (membrane, multi-domain).

Main Results:

  • Only 71 genes or orthologues were identified as easy targets for high-throughput structural studies, fewer than anticipated.
  • A significant portion of Mycoplasma proteins require homologues from other organisms for expression due to codon usage differences.
  • Membrane and large multi-domain proteins present solubility and size challenges for direct structure determination.

Conclusions:

  • The number of readily accessible protein targets for structural genomics is limited.
  • Overcoming challenges like codon bias and protein complexity requires alternative strategies for difficult targets.
  • Developing new approaches is crucial for advancing structural genomics, particularly for microbial systems.