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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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...
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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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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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RNA-seq03:21

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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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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.
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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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Novel Sequence Discovery by Subtractive Genomics
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Alignment-free sequence comparison: benefits, applications, and tools.

Andrzej Zielezinski1, Susana Vinga2, Jonas Almeida3

  • 1Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland.

Genome Biology
|October 5, 2017
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Summary
This summary is machine-generated.

Alignment-free sequence analysis offers powerful tools for genomics and protein research, especially with next-generation sequencing data. This guide clarifies their function, compares them to alignment methods, and highlights available software for researchers.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Alignment-free sequence analysis is increasingly used for diverse biological problems, including phylogeny, protein family classification, horizontal gene transfer detection, and recombination analysis.
  • These methods are particularly advantageous for processing and analyzing large-scale next-generation sequencing data due to their speed and scalability.

Purpose of the Study:

  • To clarify the working principles of alignment-free sequence analysis methods.
  • To compare alignment-free methods with traditional alignment-based approaches.
  • To provide a comprehensive guide to existing alignment-free sequence analysis tools for researchers.

Main Methods:

  • Review and synthesis of current alignment-free sequence analysis techniques.
  • Comparative analysis of alignment-free and alignment-based methodologies.
  • Survey and categorization of available software tools for alignment-free analysis.

Main Results:

  • Detailed explanation of the mechanisms underlying various alignment-free approaches.
  • Discussion on the strengths and limitations of alignment-free methods relative to alignment-based methods.
  • An organized overview of current alignment-free sequence analysis tools, aiding tool selection.

Conclusions:

  • Alignment-free methods provide efficient and effective alternatives for various sequence analysis tasks, especially in the era of big sequencing data.
  • Understanding these methods empowers researchers to select appropriate tools for their specific phylogenetic, classification, or detection needs.
  • This guide serves as a valuable resource for researchers seeking to leverage alignment-free sequence analysis in their work.