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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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...
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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Related Experiment Video

Updated: Jun 5, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter

David Raab, Marcus Graf, Frank Notka

    Systems and Synthetic Biology
    |December 31, 2010
    PubMed
    Summary
    This summary is machine-generated.

    This study introduces a novel algorithm for de novo gene synthesis, optimizing coding sequences by considering codon usage and restriction sites. The Mr. Gene web-application implements this algorithm, enabling efficient custom gene design.

    Keywords:
    Codon optimizationExpression optimizationGene synthesisSequence optimization algorithmSynthetic genes

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    Area of Science:

    • Synthetic Biology
    • Bioinformatics
    • Molecular Biology

    Background:

    • De novo gene synthesis offers freedom from natural template limitations.
    • Efficient algorithms are crucial for optimizing synthetic gene sequences based on specific requirements.
    • Adapting codon usage and avoiding restriction sites are key challenges in gene synthesis.

    Purpose of the Study:

    • To present a novel algorithm for optimizing de novo gene synthesis.
    • To develop an efficient method for calculating coding sequences with desired properties.
    • To introduce the Mr. Gene web-application as a practical implementation of the algorithm.

    Main Methods:

    • A sliding "variation window" algorithm is employed to optimize coding sequences.
    • Candidate sequences are generated by evaluating combinations of synonymous codons within the window.
    • A quality function assesses candidate sequences, and the optimal codon is selected and fixed.
    • The window slides sequentially along the coding sequence for iterative optimization.

    Main Results:

    • The algorithm effectively calculates optimized coding sequences by balancing multiple requirements.
    • The Mr. Gene web-application provides a freely accessible tool for implementing the algorithm.
    • Experimental applications demonstrate the practical utility of the developed algorithm.

    Conclusions:

    • The presented algorithm and Mr. Gene tool facilitate efficient and customized de novo gene synthesis.
    • This approach overcomes limitations of natural templates and enhances synthetic biology workflows.
    • The method allows for precise control over sequence properties like codon adaptation and restriction site avoidance.