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Selected papers from WABI 2017

Edited by Knut Reinert and Russell Schwartz

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare no competing interests.

View all collections published in Algorithms for Molecular Biology.

  1. Content type: Research

    High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these ...

    Authors: Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini and Taher Mun

    Citation: Algorithms for Molecular Biology 2019 14:13

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  2. Content type: Research

    Liquid chromatography combined with tandem mass spectrometry is an important tool in proteomics for peptide identification. Liquid chromatography temporally separates the peptides in a sample. The peptides tha...

    Authors: Yves Frank, Tomas Hruz, Thomas Tschager and Valentin Venzin

    Citation: Algorithms for Molecular Biology 2018 13:14

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  3. Content type: Research

    The double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been...

    Authors: Pijus Simonaitis and Krister M. Swenson

    Citation: Algorithms for Molecular Biology 2018 13:9

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  4. Content type: Research

    Patterns with wildcards in specified positions, namely spaced seeds, are increasingly used instead of k-mers in many bioinformatics applications that require indexing, querying and rapid similarity search, as the...

    Authors: Samuele Girotto, Matteo Comin and Cinzia Pizzi

    Citation: Algorithms for Molecular Biology 2018 13:8

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  5. Content type: Research

    An important task in a metagenomic analysis is the assignment of taxonomic labels to sequences in a sample. Most widely used methods for taxonomy assignment compare a sequence in the sample to a database of kn...

    Authors: Nidhi Shah, Stephen F. Altschul and Mihai Pop

    Citation: Algorithms for Molecular Biology 2018 13:7

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  6. Content type: Research

    For a combination of reasons (including data generation protocols, approaches to taxon and gene sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they do not contain a...

    Authors: Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati and Tandy Warnow

    Citation: Algorithms for Molecular Biology 2018 13:6

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  7. Content type: Research

    Microbial typing methods are commonly used to study the relatedness of bacterial strains. Sequence-based typing methods are a gold standard for epidemiological surveillance due to the inherent portability of s...

    Authors: João A. Carriço, Maxime Crochemore, Alexandre P. Francisco, Solon P. Pissis, Bruno Ribeiro-Gonçalves and Cátia Vaz

    Citation: Algorithms for Molecular Biology 2018 13:4

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  8. Content type: Research

    In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event-labeled gene trees. Knowledge o...

    Authors: Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke and Marc Hellmuth

    Citation: Algorithms for Molecular Biology 2018 13:2

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