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  1. Research

    Core column prediction for protein multiple sequence alignments

    In a computed protein multiple sequence alignment, the coreness of a column is the fraction of its substitutions that are in so-called core columns of the gold-standard reference alignment of its proteins. In ben...

    Dan DeBlasio and John Kececioglu

    Algorithms for Molecular Biology 2017 12:11

    Published on: 19 April 2017

  2. Research

    Gerbil: a fast and memory-efficient k-mer counter with GPU-support

    A basic task in bioinformatics is the counting of k-mers in genome sequences. Existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degra...

    Marius Erbert, Steffen Rechner and Matthias Müller-Hannemann

    Algorithms for Molecular Biology 2017 12:9

    Published on: 31 March 2017

  3. Research

    Aligning coding sequences with frameshift extension penalties

    Frameshift translation is an important phenomenon that contributes to the appearance of novel coding DNA sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of gene...

    Safa Jammali, Esaie Kuitche, Ayoub Rachati, François Bélanger, Michelle Scott and Aïda Ouangraoua

    Algorithms for Molecular Biology 2017 12:10

    Published on: 31 March 2017

  4. Software article

    The feasibility of genome-scale biological network inference using Graphics Processing Units

    Systems research spanning fields from biology to finance involves the identification of models to represent the underpinnings of complex systems. Formal approaches for data-driven identification of network int...

    Raghuram Thiagarajan, Amir Alavi, Jagdeep T. Podichetty, Jason N. Bazil and Daniel A. Beard

    Algorithms for Molecular Biology 2017 12:8

    Published on: 20 March 2017

  5. Research

    On avoided words, absent words, and their application to biological sequence analysis

    The deviation of the observed frequency of a word w from its expected frequency in a given sequence x is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguisti...

    Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas S. Iliopoulos, Manal Mohamed, Solon P. Pissis and Dimitris Polychronopoulos

    Algorithms for Molecular Biology 2017 12:5

    Published on: 14 March 2017

  6. Research

    On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model

    Phylogenetic tree reconciliation is a widely-used method for inferring the evolutionary histories of genes and species. In the duplication-loss-coalescence (DLC) model, we seek a reconciliation that explains t...

    Daniel Bork, Ricson Cheng, Jincheng Wang, Jean Sung and Ran Libeskind-Hadas

    Algorithms for Molecular Biology 2017 12:6

    Published on: 14 March 2017

  7. Research

    Approximating the DCJ distance of balanced genomes in linear time

    Rearrangements are large-scale mutations in genomes, responsible for complex changes and structural variations. Most rearrangements that modify the organization of a genome can be represented by the double cut...

    Diego P. Rubert, Pedro Feijão, Marília Dias Vieira Braga, Jens Stoye and Fábio Henrique Viduani Martinez

    Algorithms for Molecular Biology 2017 12:3

    Published on: 9 March 2017

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

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