Sequence analysis (applications)

Section edited by João Setubal

This section incorporates all aspects of sequence analysis applications, including but not limited to: software, workflows and webservers dealing with applied sequence/genome analysis, sequence assembly, analysis of sequence features, and protein function and ligand binding, estimated through sequence features.

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  1. Research article

    DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins

    Insecticide resistance is a major challenge for the control program of insect pests in the fields of crop protection, human and animal health etc. Resistance to different insecticides is conferred by the prote...

    Prabina Kumar Meher, Tanmaya Kumar Sahu, Anjali Banchariya and Atmakuri Ramakrishna Rao

    BMC Bioinformatics 2017 18:190

    Published on: 24 March 2017

  2. Software

    TreeToReads - a pipeline for simulating raw reads from phylogenies

    Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several...

    Emily Jane McTavish, James Pettengill, Steven Davis, Hugh Rand, Errol Strain, Marc Allard and Ruth E. Timme

    BMC Bioinformatics 2017 18:178

    Published on: 20 March 2017

  3. Software

    LW-FQZip 2: a parallelized reference-based compression of FASTQ files

    The rapid progress of high-throughput DNA sequencing techniques has dramatically reduced the costs of whole genome sequencing, which leads to revolutionary advances in gene industry. The explosively increasing...

    Zhi-An Huang, Zhenkun Wen, Qingjin Deng, Ying Chu, Yiwen Sun and Zexuan Zhu

    BMC Bioinformatics 2017 18:179

    Published on: 20 March 2017

  4. Software

    ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface

    Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and d...

    Anke Fähnrich, Moritz Krebbel, Normann Decker, Martin Leucker, Felix D. Lange, Kathrin Kalies and Steffen Möller

    BMC Bioinformatics 2017 18:164

    Published on: 11 March 2017

  5. Software

    A new parallel pipeline for DNA methylation analysis of long reads datasets

    DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of t...

    Ricardo Olanda, Mariano Pérez, Juan M. Orduña, Joaquín Tárraga and Joaquín Dopazo

    BMC Bioinformatics 2017 18:161

    Published on: 9 March 2017

  6. Research article

    Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides

    Several methods have been developed to predict the pathogenicity of missense mutations but none has been specifically designed for classification of variants in mtDNA-encoded polypeptides. Moreover, there is n...

    Antonio Martín-Navarro, Andrés Gaudioso-Simón, Jorge Álvarez-Jarreta, Julio Montoya, Elvira Mayordomo and Eduardo Ruiz-Pesini

    BMC Bioinformatics 2017 18:158

    Published on: 7 March 2017

  7. Software

    BBCAnalyzer: a visual approach to facilitate variant calling

    Deriving valid variant calling results from raw next-generation sequencing data is a particularly challenging task, especially with respect to clinical diagnostics and personalized medicine. However, when usin...

    Sarah Sandmann, Aniek O. de Graaf and Martin Dugas

    BMC Bioinformatics 2017 18:133

    Published on: 28 February 2017

  8. Research article

    Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing

    RNA-Seq technology has received a lot of attention in recent years for microalgal global transcriptomic profiling. It is widely used in transcriptome-wide analysis of gene expression., particularly for microal...

    Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan and Yuan Kun Lee

    BMC Bioinformatics 2017 18:122

    Published on: 22 February 2017

  9. Software

    ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data

    In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a use...

    Sergio Gonzalez, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo and Norma Paniego

    BMC Bioinformatics 2017 18:121

    Published on: 22 February 2017

  10. Software

    MARV: a tool for genome-wide multi-phenotype analysis of rare variants

    Genome-wide association studies have enabled identification of thousands of loci for hundreds of traits. Yet, for most human traits a substantial part of the estimated heritability is unexplained. This and rec...

    Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P. Morris and Inga Prokopenko

    BMC Bioinformatics 2017 18:110

    Published on: 16 February 2017

  11. Software

    VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology

    With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides ...

    Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan and Amjad Ali

    BMC Bioinformatics 2017 18:106

    Published on: 13 February 2017

  12. Software

    PyHLA: tests for the association between HLA alleles and diseases

    Recently, several tools have been designed for human leukocyte antigen (HLA) typing using single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) data. These tools provide high-throughp...

    Yanhui Fan and You-Qiang Song

    BMC Bioinformatics 2017 18:90

    Published on: 6 February 2017

  13. Software

    T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes

    Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequenc...

    Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos and Grigoris D. Amoutzias

    BMC Bioinformatics 2017 18:13

    Published on: 5 January 2017

  14. Software

    Accelerating metagenomic read classification on CUDA-enabled GPUs

    Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this cont...

    Robin Kobus, Christian Hundt, André Müller and Bertil Schmidt

    BMC Bioinformatics 2017 18:11

    Published on: 3 January 2017

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