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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...
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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.
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GSDS 2.0: an upgraded gene feature visualization server.

Bo Hu1, Jinpu Jin2, An-Yuan Guo2

  • 1State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China, College of Life Science, Beijing Normal University, Beijing 100875, People's Republic of China and Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.

Bioinformatics (Oxford, England)
|December 16, 2014
PubMed
Summary
This summary is machine-generated.

The Gene Structure Display Server (GSDS) 2.0 offers an upgraded interface and enhanced features for visualizing gene structures and annotations. This tool aids biologists in intuitive investigation of gene function and evolution, now with added phylogenetic tree integration.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Gene structure visualization is crucial for understanding gene function and evolution.
  • The Gene Structure Display Server (GSDS) has been a valuable tool for biologists since 2007.
  • Previous versions of GSDS have served over 60,000 users.

Purpose of the Study:

  • To report the upgraded Gene Structure Display Server (GSDS) 2.0.
  • To introduce enhanced features for gene structure and annotation visualization.
  • To provide an integrated platform for evolutionary analysis of genes.

Main Methods:

  • Development of a newly designed user interface for GSDS 2.0.
  • Implementation of support for more annotation feature types and data formats.
  • Integration of a visual editor for modifying generated figures.
  • Addition of functionality to incorporate user-specified phylogenetic trees.

Main Results:

  • GSDS 2.0 features a modernized interface for improved usability.
  • The upgraded server supports a wider range of annotation features and formats.
  • An integrated visual editor allows for direct manipulation of gene structure figures.
  • Phylogenetic tree integration facilitates comparative evolutionary studies.

Conclusions:

  • GSDS 2.0 represents a significant advancement in gene structure visualization tools.
  • The enhanced features and usability of GSDS 2.0 will further support biological research.
  • The availability of source code promotes transparency and further development in the field.