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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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.
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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus
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Next-generation sequence assembly: four stages of data processing and computational challenges.

Sara El-Metwally1, Taher Hamza1, Magdi Zakaria1

  • 1Computer Science Department, Faculty of Computers and Information, Mansoura University, Mansoura, Egypt.

Plos Computational Biology
|December 19, 2013
PubMed
Summary
This summary is machine-generated.

Next-generation sequencing (NGS) accelerates genomic research, but assembling the resulting DNA reads is challenging. This review outlines a four-stage framework for NGS genome assemblers and discusses current challenges and solutions.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) technologies have revolutionized genomic research due to high throughput and reduced costs.
  • However, assembling the vast amounts of short DNA reads generated by NGS remains a significant computational challenge.

Purpose of the Study:

  • To review the fundamental framework of next-generation genome sequence assemblers.
  • To survey techniques, algorithms, and software tools used in each stage of the assembly process.
  • To identify current challenges and the state-of-the-art in NGS genome assembly.

Main Methods:

  • The review analyzes genome assembly through a four-stage framework: preprocessing filtering, graph construction, graph simplification, and postprocessing filtering.
  • It surveys various computational techniques and software employed at each stage.
  • The current state-of-the-art and challenges are discussed within this framework.

Main Results:

  • The review details the four core stages involved in next-generation genome sequence assembly.
  • It highlights the diversity of algorithms and tools applicable to each stage.
  • Key challenges facing current assemblers are identified, providing insight into the field's limitations.

Conclusions:

  • A four-stage framework provides a comprehensive view of next-generation genome sequence assemblers.
  • Addressing identified challenges is crucial for advancing genome assembly.
  • A layered architecture approach is recommended for developing versatile assemblers adaptable to various sequencing platforms.