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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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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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RNA-seq03:21

RNA-seq

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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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DNA-only Transposons02:57

DNA-only Transposons

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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
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lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

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Translesion DNA Polymerases02:10

Translesion DNA Polymerases

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Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
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Related Experiment Video

Updated: May 7, 2025

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

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Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses.

Xiaoyu Guo1, Zhenming Wu1, Shu Zhang1

  • 1School of Computer Science and Technology, Qingdao University, Ningxia Road, Qingdao, Shandong Province, 266071, China.

BMC Genomics
|December 30, 2024
PubMed
Summary

Cov-trans accurately assembles coronavirus transcripts, overcoming limitations of existing methods. This novel tool enhances viral transcript boundary identification for improved virology research and antiviral development.

Keywords:
CoronavirusesDiscontinuous transcriptionMixed integer linear programmingReferenced-based assembly

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Area of Science:

  • Virology
  • Computational Biology
  • Bioinformatics

Background:

  • Coronaviruses utilize discontinuous transcription for efficient replication and host cell transmission.
  • Accurate viral transcript assembly is vital for virology research and developing antiviral strategies.
  • Existing transcript assembly algorithms, designed for eukaryotes, are ill-suited for coronaviruses, leading to low accuracy in transcript boundary determination.

Purpose of the Study:

  • To develop a highly accurate viral transcript assembly algorithm specifically for coronaviruses.
  • To address the limitations of current methods in determining viral transcript boundaries.

Main Methods:

  • Propose Cov-trans, a reference-based transcript assembler for coronavirus discontinuous transcription.
  • Identify canonical transcripts using discontinuous transcription mechanisms, start/stop codons, and read alignment.
  • Formulate non-canonical transcript assembly as a path extraction problem using mixed integer linear programming.

Main Results:

  • Cov-trans demonstrates superior accuracy and recall compared to other assemblers.
  • Cov-trans excels at accurately identifying viral transcript boundaries.
  • The developed algorithm effectively recovers non-canonical viral transcripts.

Conclusions:

  • Cov-trans offers a significant advancement in assembling coronavirus transcripts.
  • The tool's high accuracy in boundary identification is a key strength.
  • Cov-trans is available for use in virology research and antiviral development.