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. Methodology Article

    De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline

    The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together...

    You-Yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen and Hurng-Yi Wang

    BMC Bioinformatics 2017 18:223

    Published on: 26 April 2017

  2. Software

    An auditory display tool for DNA sequence analysis

    DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorith...

    Mark D. Temple

    BMC Bioinformatics 2017 18:221

    Published on: 24 April 2017

  3. Research Article

    Meta-analysis approach as a gene selection method in class prediction: does it improve model performance? A case study in acute myeloid leukemia

    Aggregating gene expression data across experiments via meta-analysis is expected to increase the precision of the effect estimates and to increase the statistical power to detect a certain fold change. This s...

    Putri W. Novianti, Victor L. Jong, Kit C. B. Roes and Marinus J. C. Eijkemans

    BMC Bioinformatics 2017 18:210

    Published on: 11 April 2017

  4. Research Article

    A machine learning approach for viral genome classification

    Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification and annotation of these genomes constitute important assets in the discovery of genomic variabil...

    Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani and Abdoulaye Baniré Diallo

    BMC Bioinformatics 2017 18:208

    Published on: 11 April 2017

  5. Software

    HALC: High throughput algorithm for long read error correction

    The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correcti...

    Ergude Bao and Lingxiao Lan

    BMC Bioinformatics 2017 18:204

    Published on: 5 April 2017

  6. Methodology Article

    Significance evaluation in factor graphs

    Factor graphs provide a flexible and general framework for specifying probability distributions. They can capture a range of popular and recent models for analysis of both genomics data as well as data from ot...

    Tobias Madsen, Asger Hobolth, Jens Ledet Jensen and Jakob Skou Pedersen

    BMC Bioinformatics 2017 18:199

    Published on: 31 March 2017

  7. 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

    The Erratum to this article has been published in BMC Bioinformatics 2017 18:222

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

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