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Related Concept Videos

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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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...

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Related Experiment Video

Updated: May 22, 2026

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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SIS: a program to generate draft genome sequence scaffolds for prokaryotes.

Zanoni Dias1, Ulisses Dias, João C Setubal

  • 1Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil. setubal@iq.usp.br.

BMC Bioinformatics
|May 16, 2012
PubMed
Summary
This summary is machine-generated.

A new algorithm and tool called sis accurately generates prokaryotic genome scaffolds by identifying large-scale inversions. This method improves genome assembly and comparison, even with complex rearrangements.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Decreasing DNA sequencing costs lead to more prokaryotic draft genomes.
  • Contig scaffolds aid genome comparison and gap closure.
  • Mapping to reference genomes can fail due to rearrangements like inversions.

Purpose of the Study:

  • Develop a linear-time algorithm for generating contig scaffolds for draft prokaryotic genomes.
  • Address challenges posed by large-scale inversions in genome assembly.
  • Improve the accuracy of scaffold generation compared to existing methods.

Main Methods:

  • Developed a linear-time algorithm utilizing 'inversion signatures' to detect large-scale inversions.
  • Implemented the algorithm in a tool named sis.
  • Compared sis performance against seven other scaffold-generating programs.

Main Results:

  • The sis algorithm correctly generates scaffolds when inversion signatures are present and intact.
  • Scaffolds can be generated even with inversions, though accuracy may vary.
  • sis demonstrated superior performance compared to seven other scaffold-generating programs in tests.

Conclusions:

  • sis is a user-friendly tool for generating contig scaffolds, available as stand-alone software and a web server.
  • The tool's performance supports the prevalence of large-scale inversions in prokaryotic genomes.