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Related Concept Videos

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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Genome Copying Errors02:46

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DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Sanger Sequencing01:57

Sanger Sequencing

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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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Next-generation Sequencing03:00

Next-generation Sequencing

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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.
Next-Generation Sequencing Methods
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The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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Updated: Jun 6, 2025

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
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Collinearity-based Assembly Correction Tool GUI: Software for collinearity-based genome assembly correction.

Shengcheng Zhang1,2, Hejun Du1, Xingtan Zhang2

  • 1Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China.

G3 (Bethesda, Md.)
|November 22, 2024
PubMed
Summary
This summary is machine-generated.

Genome assembly errors impact downstream analyses. The Collinearity-based Assembly Correction Tool GUI corrects these errors using reference genome collinearity, offering manual and automatic adjustments for improved genome accuracy.

Keywords:
Python softwarealgorithmgenome assemblymanually correction

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Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology

Background:

  • Genome assembly errors can significantly compromise the reliability of subsequent genomic analyses.
  • Accurate genome assemblies are crucial for understanding genetic variation, evolution, and disease.

Purpose of the Study:

  • To introduce the Collinearity-based Assembly Correction Tool Graphical User Interface (GUI) for rectifying genome assembly errors.
  • To provide a user-friendly platform for manual and automated correction of large-scale assembly defects, particularly in polyploid genomes.

Main Methods:

  • Leveraging collinearity information between an assembled genome and a reference genome.
  • Implementing a GUI that supports manual correction operations: insertion, deletion, inversion, and swapping of contigs and chromosomes.
  • Automated reclustering, relabeling, and redrawing of the assembly post-modification for change tracking.

Main Results:

  • The tool enables efficient visualization and correction of genome assembly errors.
  • Advanced collinearity detection capabilities facilitate the identification and resolution of large-scale assembly issues.
  • The software supports robust error correction in complex polyploid genome assemblies.

Conclusions:

  • The Collinearity-based Assembly Correction Tool GUI is an effective solution for improving genome assembly quality.
  • Its user-friendly interface and advanced features make it valuable for genomic research, especially for polyploid organisms.