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Related Concept Videos

Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
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Overview
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...

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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
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GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events.

Te-Chin Chu1, Tsunglin Liu, D T Lee

  • 1Institute of Information Science, Academia Sinica, National Taiwan University, Taipei, Taiwan.

Bioinformatics (Oxford, England)
|June 23, 2009
PubMed
Summary
This summary is machine-generated.

Genomic Rearrangement Aligner (GR-Aligner) identifies breakpoints in homologous sequences, revealing patterns near rearrangements. This tool aids in studying evolutionary mechanisms and biological functions of genomic rearrangements.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Homologous genomic sequences across species often exhibit varied rearrangement events.
  • Identifying specific breakpoint patterns driving these rearrangements requires nucleotide-level precision.
  • Existing alignment tools lack the capability to precisely locate breakpoints and analyze flanking sequences.

Purpose of the Study:

  • To develop an effective and efficient algorithm for identifying breakpoints in homologous sequences.
  • To provide detailed nucleotide-level alignments of sequences surrounding rearrangement breakpoints.
  • To facilitate the study of evolutionary mechanisms and biological functions associated with genomic rearrangements.

Main Methods:

  • Developed GR-Aligner (Genomic Rearrangement Aligner), a novel pairwise sequence alignment algorithm.
  • Integrated forward and reverse alignments of homologous sequences flanking rearrangement breakpoints.
  • Implemented an option to extend sequence alignments to the identified breakpoints.

Main Results:

  • GR-Aligner accurately identifies breakpoints in homologous sequences.
  • The algorithm provides detailed alignments of sequences in breakpoint regions.
  • Outputs enable in-depth analysis of evolutionary patterns and functional significance of rearrangements.

Conclusions:

  • GR-Aligner is an effective tool for pinpointing genomic rearrangement breakpoints.
  • The detailed alignments generated by GR-Aligner support research into sequence evolution.
  • This tool enhances our understanding of the mechanisms and functions underlying genomic rearrangements.