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Research
The basic RNA secondary structure prediction problem or single sequence folding problem (SSF) was solved 35 years ago by a now well-known
Algorithms for Molecular Biology 2016 11:22
Published on: 5 August 2016
Erratum
Algorithms for Molecular Biology 2016 11:21
Published on: 27 July 2016
The original article was published in Algorithms for Molecular Biology 2016 11:12
Research
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...
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
Research
Metagenomics enables the analysis of bacterial population composition and the study of emergent population features, such as shared metabolic pathways. Recently, we have shown that metagenomics datasets can be...
Algorithms for Molecular Biology 2016 11:19
Published on: 8 July 2016
Research
Superpositioning is an important problem in structural biology. Determining an optimal superposition requires a one-to-one correspondence between the atoms of two proteins structures. However, in practice, som...
Algorithms for Molecular Biology 2016 11:18
Published on: 21 June 2016
Research
The analysis of correlation in alignments generates a matrix of predicted contacts between positions in the structure and while these can arise for many reasons, the simplest explanation is that the pair of re...
Algorithms for Molecular Biology 2016 11:17
Published on: 18 June 2016
Research
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...
Algorithms for Molecular Biology 2016 11:16
Published on: 1 June 2016
Research
Recent coevolutionary analysis has considered tree topology as a means to reduce the asymptotic complexity associated with inferring the complex coevolutionary interrelationships that arise between phylogeneti...
Algorithms for Molecular Biology 2016 11:15
Published on: 21 May 2016
Research
Despite the recognized importance of module discovery in biological networks to enhance our understanding of complex biological systems, existing methods generally suffer from two major drawbacks. First, there...
Algorithms for Molecular Biology 2016 11:14
Published on: 20 May 2016
Research
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...
Algorithms for Molecular Biology 2016 11:13
Published on: 17 May 2016
Research
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...
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
Research
The mutual exclusivity of somatic genome alterations (SGAs), such as somatic mutations and copy number alterations, is an important observation of tumors and is widely used to search for cancer signaling pathw...
Algorithms for Molecular Biology 2016 11:11
Published on: 4 May 2016
Software article
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...
Algorithms for Molecular Biology 2016 11:10
Published on: 3 May 2016
Research article
RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to i...
Algorithms for Molecular Biology 2016 11:7
Published on: 23 April 2016
Research
Suffix arrays and their variants are used widely for representing genomes in search applications. Enhanced suffix arrays (ESAs) provide fast search speed, but require large auxiliary data structures for storin...
Algorithms for Molecular Biology 2016 11:9
Published on: 23 April 2016
Research
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...
Algorithms for Molecular Biology 2016 11:8
Published on: 23 April 2016
Research
Measuring sequence similarity is central for many problems in bioinformatics. In several contexts alignment-free techniques based on exact occurrences of substrings are faster, but also less accurate, than ali...
Algorithms for Molecular Biology 2016 11:6
Published on: 21 April 2016
Research
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...
Algorithms for Molecular Biology 2016 11:5
Published on: 18 April 2016
Research
While tree-oriented methods for inferring orthology and paralogy relations between genes are based on reconciling a gene tree with a species tree, many tree-free methods are also available (usually based on se...
Algorithms for Molecular Biology 2016 11:4
Published on: 16 April 2016
Research
High throughput sequencing technologies have become fast and cheap in the past years. As a result, large-scale projects started to sequence tens to several thousands of genomes per species, producing a high nu...
Algorithms for Molecular Biology 2016 11:3
Published on: 14 April 2016
Software article
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...
Algorithms for Molecular Biology 2016 11:2
Published on: 11 March 2016
Research
The accurate annotation of genes in newly sequenced genomes remains a challenge. Although sophisticated comparative pipelines are available, computationally derived gene models are often less than perfect. Thi...
Algorithms for Molecular Biology 2016 11:1
Published on: 24 February 2016
Software article
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...
Algorithms for Molecular Biology 2015 10:31
Published on: 30 December 2015
Software article
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...
Algorithms for Molecular Biology 2015 10:30
Published on: 23 December 2015
Research
The rational, in silico prediction of gene-knockouts to turn organisms into efficient cell factories is an essential and computationally challenging task in metabolic engineering. Elementary flux mode analys...
Algorithms for Molecular Biology 2015 10:29
Published on: 21 December 2015
