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  1. Research

    A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

    Recently, Marcus et al. (Bioinformatics 30:3476–83, 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related s...

    Timo Beller and Enno Ohlebusch

    Algorithms for Molecular Biology 2016 11:20

    Published on: 18 July 2016

    The Erratum to this article has been published in Algorithms for Molecular Biology 2016 11:28

  2. Research

    Identification of donor splice sites using support vector machine: a computational approach based on positional, compositional and dependency features

    Identification of splice sites is essential for annotation of genes. Though existing approaches have achieved an acceptable level of accuracy, still there is a need for further improvement. Besides, most of th...

    Prabina Kumar Meher, Tanmaya Kumar Sahu, A. R. Rao and S. D. Wahi

    Algorithms for Molecular Biology 2016 11:16

    Published on: 1 June 2016

  3. Research

    Models and algorithms for genome rearrangement with positional constraints

    Traditionally, the merit of a rearrangement scenario between two gene orders has been measured based on a parsimony criteria alone; two scenarios with the same number of rearrangements are considered equally g...

    Krister M. Swenson, Pijus Simonaitis and Mathieu Blanchette

    Algorithms for Molecular Biology 2016 11:13

    Published on: 17 May 2016

  4. Research

    Circular sequence comparison: algorithms and applications

    Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in seq...

    Roberto Grossi, Costas S. Iliopoulos, Robert Mercas, Nadia Pisanti, Solon P. Pissis, Ahmad Retha and Fatima Vayani

    Algorithms for Molecular Biology 2016 11:12

    Published on: 10 May 2016

    The Erratum to this article has been published in Algorithms for Molecular Biology 2016 11:21

  5. Software article

    Jabba: hybrid error correction for long sequencing reads

    Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, un...

    Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert and Jan Fostier

    Algorithms for Molecular Biology 2016 11:10

    Published on: 3 May 2016

  6. Research

    RNA folding with hard and soft constraints

    A large class of RNA secondary structure prediction programs uses an elaborate energy model grounded in extensive thermodynamic measurements and exact dynamic programming algorithms. External experimental evid...

    Ronny Lorenz, Ivo L. Hofacker and Peter F. Stadler

    Algorithms for Molecular Biology 2016 11:8

    Published on: 23 April 2016

  7. Research

    Bitpacking techniques for indexing genomes: I. Hash tables

    Hash tables constitute a widely used data structure for indexing genomes that provides a list of genomic positions for each possible oligomer of a given size. The offset array in a hash table grows exponential...

    Thomas D. Wu

    Algorithms for Molecular Biology 2016 11:5

    Published on: 18 April 2016

  8. Software article

    Estimation of genetic diversity in viral populations from next generation sequencing data with extremely deep coverage

    In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motiva...

    Jean P. Zukurov, Sieberth do Nascimento-Brito, Angela C. Volpini, Guilherme C. Oliveira, Luiz Mario R. Janini and Fernando Antoneli

    Algorithms for Molecular Biology 2016 11:2

    Published on: 11 March 2016

  9. Software article

    Interpretation and approximation tools for big, dense Markov chain transition matrices in population genetics

    Markov chains are a common framework for individual-based state and time discrete models in evolution. Though they played an important role in the development of basic population genetic theory, the analysis o...

    Katja Reichel, Valentin Bahier, Cédric Midoux, Nicolas Parisey, Jean-Pierre Masson and Solenn Stoeckel

    Algorithms for Molecular Biology 2015 10:31

    Published on: 30 December 2015

  10. Software article

    HIA: a genome mapper using hybrid index-based sequence alignment

    A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapid...

    Jongpill Choi, Kiejung Park, Seong Beom Cho and Myungguen Chung

    Algorithms for Molecular Biology 2015 10:30

    Published on: 23 December 2015

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