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Related Concept Videos

RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...

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Related Experiment Video

Updated: Jun 21, 2026

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
14:26

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

CSA: an efficient algorithm to improve circular DNA multiple alignment.

Francisco Fernandes1, Luísa Pereira, Ana T Freitas

  • 1Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), Lisboa, Portugal. fjdf@kdbio.inesc-id.pt

BMC Bioinformatics
|July 25, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a new algorithm to improve phylogenetic analysis by correctly aligning circular DNA sequences. The method enhances the accuracy of evolutionary comparisons between species using multiple sequence alignment.

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Last Updated: Jun 21, 2026

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Comparative genomics relies on aligning homologous sequences to reconstruct evolutionary history.
  • Multiple sequence alignment (MSA) is crucial for analyzing genomic data, especially mitochondrial DNA (mtDNA).
  • Existing MSA algorithms primarily handle linear DNA, posing challenges for circular genomes like mtDNA.

Purpose of the Study:

  • To develop an efficient algorithm for pre-processing circular DNA sequences for improved MSA.
  • To address the limitations of current MSA tools in handling circular genomes.
  • To enhance the accuracy of phylogenetic analyses derived from circular DNA.

Main Methods:

  • Proposed an algorithm to identify optimal cutting points in circular genomes for linearization.
  • The algorithm finds the longest common non-repeated subsequences across multiple circular DNA sequences.
  • Circular sequences were rotated and linearized before applying standard MSA tools (CLUSTALW, MAVID).

Main Results:

  • The proposed algorithm successfully identified optimal regions for cutting circular mtDNA sequences.
  • Pre-processing circular DNA with the algorithm significantly improved MSA efficiency and alignment quality.
  • Phylogenetic comparisons using the new method yielded more realistic evolutionary interpretations.

Conclusions:

  • A circularization and rotation pre-processing step is essential for efficient MSA of circular DNA.
  • The developed algorithm enhances the performance of existing MSA tools for phylogenetic studies.
  • This approach leads to more accurate and reliable evolutionary insights from genomic data.