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Related Concept Videos

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DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
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Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is...
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Related Experiment Video

Updated: Oct 20, 2025

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
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Extraction of Long k-mers Using Spaced Seeds.

Miika Leinonen, Leena Salmela

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |September 16, 2021
    PubMed
    Summary
    This summary is machine-generated.

    LoMeX accurately extracts long DNA k-mers using spaced seeds, even with sequencing errors. This bioinformatics tool maintains performance as read lengths increase, outperforming standard k-mer counters.

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    Area of Science:

    • Bioinformatics
    • Genomics
    • Computational Biology

    Background:

    • K-mer extraction is crucial for DNA sequence analysis, particularly in de Bruijn graph methods.
    • Longer k-mers improve accuracy but are limited by sequencing error rates as read lengths increase.

    Purpose of the Study:

    • To develop a method for accurate long k-mer extraction from DNA reads, robust to sequencing errors.
    • To evaluate the performance of the proposed method against standard k-mer counting tools.

    Main Methods:

    • The LoMeX method utilizes spaced seeds for identifying and extracting long k-mers.
    • Experimental validation was performed using current Illumina sequencing reads and simulated data with varying read lengths.

    Main Results:

    • LoMeX achieves comparable or higher recall for long k-mer extraction from Illumina reads compared to standard tools.
    • LoMeX demonstrates sustained performance with increasing read lengths, unlike standard k-mer counters whose performance declines.

    Conclusions:

    • LoMeX provides an effective solution for accurate long k-mer extraction in the presence of sequencing errors.
    • The method is particularly valuable for future sequencing technologies with longer read lengths, overcoming limitations of current approaches.