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  1. Research

    Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

    The main challenge in de novo genome assembly of DNA-seq data is certainly to deal with repeats that are longer than the reads. In de novo transcriptome assembly of RNA-seq reads, on the other hand, this prob...

    Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele, Marie-France Sagot and Vincent Lacroix

    Algorithms for Molecular Biology 2017 12:2

    Published on: 22 February 2017

  2. Software article

    An efficient algorithm for protein structure comparison using elastic shape analysis

    Protein structure comparison play important role in in silico functional prediction of a new protein. It is also used for understanding the evolutionary relationships among proteins. A variety of methods have ...

    S. Srivastava, S. B. Lal, D. C. Mishra, U. B. Angadi, K. K. Chaturvedi, S. N. Rai and A. Rai

    Algorithms for Molecular Biology 2016 11:27

    Published on: 29 September 2016

  3. Research

    Analysis of gene copy number changes in tumor phylogenetics

    Evolution of cancer cells is characterized by large scale and rapid changes in the chromosomal  landscape. The fluorescence in situ hybridization (FISH) technique provides a way to measure the copy numbers of ...

    Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins, Bing Feng and Jijun Tang

    Algorithms for Molecular Biology 2016 11:26

    Published on: 22 September 2016

  4. Research

    Enumeration of minimal stoichiometric precursor sets in metabolic networks

    What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal ...

    Ricardo Andrade, Martin Wannagat, Cecilia C. Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo V. Milreu, Leen Stougie and Marie-France Sagot

    Algorithms for Molecular Biology 2016 11:25

    Published on: 19 September 2016

  5. Research

    Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis

    Pyrosequencing Allele Quantification (AQ) is a cost-effective DNA sequencing method that can be used for detecting somatic mutations in formalin-fixed paraffin-embedded (FFPE) samples. The method displays a lo...

    Jerome Ambroise, Jamal Badir, Louise Nienhaus, Annie Robert, Anne-France Dekairelle and Jean-Luc Gala

    Algorithms for Molecular Biology 2016 11:24

    Published on: 15 September 2016

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

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