Sequence analysis (methods)

Section edited by Olivier Poch

This section incorporates all aspects of sequence analysis methodology, including but not limited to: sequence alignment algorithms, discrete algorithms, phylogeny algorithms, gene prediction and sequence clustering methods.

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  1. Research article

    Genomic prediction using subsampling

    Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fittin...

    Alencar Xavier, Shizhong Xu, William Muir and Katy Martin Rainey

    BMC Bioinformatics 2017 18:191

    Published on: 24 March 2017

  2. Software

    microclass: an R-package for 16S taxonomy classification

    Taxonomic classification based on the 16S rRNA gene sequence is important for the profiling of microbial communities. In addition to giving the best possible accuracy, it is also important to quantify uncertai...

    Kristian Hovde Liland, Hilde Vinje and Lars Snipen

    BMC Bioinformatics 2017 18:172

    Published on: 16 March 2017

  3. Methodology Article

    Subgroup detection in genotype data using invariant coordinate selection

    The current gold standard in dimension reduction methods for high-throughput genotype data is the Principle Component Analysis (PCA). The presence of PCA is so dominant, that other methods usually cannot be fo...

    Daniel Fischer, Mervi Honkatukia, Maria Tuiskula-Haavisto, Klaus Nordhausen, David Cavero, Rudolf Preisinger and Johanna Vilkki

    BMC Bioinformatics 2017 18:173

    Published on: 16 March 2017

  4. Methodology Article

    Ultra-high dimensional variable selection with application to normative aging study: DNA methylation and metabolic syndrome

    Metabolic syndrome has become a major public health challenge worldwide. The association between metabolic syndrome and DNA methylation is of great research interest.

    Grace Yoon, Yinan Zheng, Zhou Zhang, Haixiang Zhang, Tao Gao, Brian Joyce, Wei Zhang, Weihua Guan, Andrea A. Baccarelli, Wenxin Jiang, Joel Schwartz, Pantel S. Vokonas, Lifang Hou and Lei Liu

    BMC Bioinformatics 2017 18:156

    Published on: 7 March 2017

  5. Methodology article

    SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data

    Targeted next-generation sequencing (NGS) has been widely used as a cost-effective way to identify the genetic basis of human disorders. Copy number variations (CNVs) contribute significantly to human genomic ...

    Yong Chen, Li Zhao, Yi Wang, Ming Cao, Violet Gelowani, Mingchu Xu, Smriti A. Agrawal, Yumei Li, Stephen P. Daiger, Richard Gibbs, Fei Wang and Rui Chen

    BMC Bioinformatics 2017 18:147

    Published on: 3 March 2017

  6. Methodology Article

    Model based heritability scores for high-throughput sequencing data

    Heritability of a phenotypic or molecular trait measures the proportion of variance that is attributable to genotypic variance. It is an important concept in breeding and genetics. Few methods are available fo...

    Pratyaydipta Rudra, W. Jenny Shi, Brian Vestal, Pamela H. Russell, Aaron Odell, Robin D. Dowell, Richard A. Radcliffe, Laura M. Saba and Katerina Kechris

    BMC Bioinformatics 2017 18:143

    Published on: 2 March 2017

  7. Methodology article

    Statistical method to compare massive parallel sequencing pipelines

    Today, sequencing is frequently carried out by Massive Parallel Sequencing (MPS) that cuts drastically sequencing time and expenses. Nevertheless, Sanger sequencing remains the main validation method to confir...

    MH. Elsensohn, N. Leblay, S. Dimassi, A. Campan-Fournier, A. Labalme, F. Roucher-Boulez, D. Sanlaville, G. Lesca, C. Bardel and P. Roy

    BMC Bioinformatics 2017 18:139

    Published on: 1 March 2017

  8. Methodology article

    3D: diversity, dynamics, differential testing – a proposed pipeline for analysis of next-generation sequencing T cell repertoire data

    Cancer immunotherapy has demonstrated significant clinical activity in different cancers. T cells represent a crucial component of the adaptive immune system and are thought to mediate anti-tumoral immunity. A...

    Li Zhang, Jason Cham, Alan Paciorek, James Trager, Nadeem Sheikh and Lawrence Fong

    BMC Bioinformatics 2017 18:129

    Published on: 27 February 2017

  9. Research Article

    Meta-aligner: long-read alignment based on genome statistics

    Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducin...

    Damoon Nashta-ali, Ali Aliyari, Ahmad Ahmadian Moghadam, Mohammad Amin Edrisi, Seyed Abolfazl Motahari and Babak Hossein Khalaj

    BMC Bioinformatics 2017 18:126

    Published on: 23 February 2017

  10. Software

    TipMT: Identification of PCR-based taxon-specific markers

    Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attr...

    Gabriela F. Rodrigues-Luiz, Mariana S. Cardoso, Hugo O. Valdivia, Edward V. Ayala, Célia M. F. Gontijo, Thiago de S. Rodrigues, Ricardo T. Fujiwara, Robson S. Lopes and Daniella C. Bartholomeu

    BMC Bioinformatics 2017 18:104

    Published on: 11 February 2017

  11. Methodology article

    Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

    Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic p...

    O. Pipek, D. Ribli, J. Molnár, Á. Póti, M. Krzystanek, A. Bodor, G. E. Tusnády, Z. Szallasi, I. Csabai and D. Szüts

    BMC Bioinformatics 2017 18:73

    Published on: 31 January 2017

  12. Methodology Article

    Disorder recognition in clinical texts using multi-label structured SVM

    Information extraction in clinical texts enables medical workers to find out problems of patients faster as well as makes intelligent diagnosis possible in the future. There has been a lot of work about disord...

    Wutao Lin, Donghong Ji and Yanan Lu

    BMC Bioinformatics 2017 18:75

    Published on: 31 January 2017

  13. Methodology Article

    Eigen-Epistasis for detecting gene-gene interactions

    A large amount of research has been devoted to the detection and investigation of epistatic interactions in genome-wide association studies (GWASs). Most of the literature focuses on low-order interactions bet...

    Virginie Stanislas, Cyril Dalmasso and Christophe Ambroise

    BMC Bioinformatics 2017 18:54

    Published on: 23 January 2017

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