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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
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...
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.
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Evolutionary Relationships through Genome Comparisons

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Sanger Sequencing

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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Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.

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Introductory Analysis and Validation of CUT&RUN Sequencing Data
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SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.

Michael S Barker1, Katrina M Dlugosch, A Chaitanya C Reddy

  • 1Botany Department, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada. msbarker@indiana.edu

Bioinformatics (Oxford, England)
|January 9, 2009
PubMed
Summary

Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a new tool for evolutionary genomics. It helps assemble 454 EST sequences using reference genomes, improving contig assembly for complex genomic data.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Next-generation sequencing (NGS) technologies generate large datasets.
  • De novo assembly of short reads can result in fragmented genomes.
  • Specific challenges exist in assembling Roche 454 EST sequences.

Purpose of the Study:

  • To develop a novel sequence assembly tool for evolutionary genomics.
  • To improve the assembly of Roche 454 EST sequences.
  • To facilitate the use of reference sequences for scaffolding.

Main Methods:

  • Development of Scaffolded and Corrected Assembly of Roche 454 (SCARF) software.
  • Utilizing high-quality reference sequences from related species.
  • Employing a reference sequence library to orient 454 sequences.

Main Results:

  • SCARF effectively knits together 454 contigs that fail traditional de novo assembly.
  • The tool enhances the assembly process by using reference-guided scaffolding.
  • Improved contiguity and accuracy in sequence assembly.

Conclusions:

  • Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a valuable tool for evolutionary genomics.
  • SCARF addresses limitations in de novo assembly for 454 EST data.
  • The software aids in reconstructing more complete genomes from NGS data.