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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. Research

    A polynomial time algorithm for computing the area under a GDT curve

    Progress in the field of protein three-dimensional structure prediction depends on the development of new and improved algorithms for measuring the quality of protein models. Perhaps the best descriptor of the...

    Aleksandar Poleksic

    Algorithms for Molecular Biology 2015 10:27

    Published on: 26 October 2015

  10. Research

    Instability in progressive multiple sequence alignment algorithms

    Progressive alignment is the standard approach used to align large numbers of sequences. As with all heuristics, this involves a tradeoff between alignment accuracy and computation time.

    Kieran Boyce, Fabian Sievers and Desmond G. Higgins

    Algorithms for Molecular Biology 2015 10:26

    Published on: 9 October 2015

  11. Research

    A multiobjective approach for identifying protein complexes and studying their association in multiple disorders

    Detecting protein complexes within protein–protein interaction (PPI) networks is a major step toward the analysis of biological processes and pathways. Identification and characterization of protein complexes ...

    Sanghamitra Bandyopadhyay, Sumanta Ray, Anirban Mukhopadhyay and Ujjwal Maulik

    Algorithms for Molecular Biology 2015 10:24

    Published on: 9 August 2015

  12. Research

    Inferring interaction type in gene regulatory networks using co-expression data

    Knowledge of interaction types in biological networks is important for understanding the functional organization of the cell. Currently information-based approaches are widely used for inferring gene regulator...

    Pegah Khosravi, Vahid H Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaei and Gary D Bader

    Algorithms for Molecular Biology 2015 10:23

    Published on: 8 July 2015

    The Erratum to this article has been published in Algorithms for Molecular Biology 2015 10:25

  13. Research

    Pareto optimization in algebraic dynamic programming

    Pareto optimization combines independent objectives by computing the Pareto front of its search space, defined as the set of all solutions for which no other candidate solution scores better under all objectives....

    Cédric Saule and Robert Giegerich

    Algorithms for Molecular Biology 2015 10:22

    Published on: 7 July 2015

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