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

    DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

    The development of single-cell RNA sequencing has enabled profound discoveries in biology, ranging from the dissection of the composition of complex tissues to the identification of novel cell types and dynami...

    Zhuo Wang, Shuilin Jin, Guiyou Liu, Xiurui Zhang, Nan Wang, Deliang Wu, Yang Hu, Chiping Zhang, Qinghua Jiang, Li Xu and Yadong Wang

    BMC Bioinformatics 2017 18:270

    Published on: 23 May 2017

  2. Research Article

    Coordinates and intervals in graph-based reference genomes

    It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represe...

    Knut D. Rand, Ivar Grytten, Alexander J. Nederbragt, Geir O. Storvik, Ingrid K. Glad and Geir K. Sandve

    BMC Bioinformatics 2017 18:263

    Published on: 18 May 2017

  3. Research Article

    The rainfall plot: its motivation, characteristics and pitfalls

    A visualization referred to as rainfall plot has recently gained popularity in genome data analysis. The plot is mostly used for illustrating the distribution of somatic cancer mutations along a reference geno...

    Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig and Geir Kjetil Sandve

    BMC Bioinformatics 2017 18:264

    Published on: 18 May 2017

  4. Methodology Article

    HLAscan: genotyping of the HLA region using next-generation sequencing data

    Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, ...

    Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim and Jongsun Jung

    BMC Bioinformatics 2017 18:258

    Published on: 12 May 2017

  5. Commentary

    Solving the master equation for Indels

    Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that a...

    Ian H. Holmes

    BMC Bioinformatics 2017 18:255

    Published on: 12 May 2017

  6. Software

    ImmunoNodes – graphical development of complex immunoinformatics workflows

    Immunoinformatics has become a crucial part in biomedical research. Yet many immunoinformatics tools have command line interfaces only and can be difficult to install. Web-based immunoinformatics tools, on the...

    Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer and Oliver Kohlbacher

    BMC Bioinformatics 2017 18:242

    Published on: 8 May 2017

  7. Research Article

    A time series driven decomposed evolutionary optimization approach for reconstructing large-scale gene regulatory networks based on fuzzy cognitive maps

    Reconstructing gene regulatory networks (GRNs) from expression data plays an important role in understanding the fundamental cellular processes and revealing the underlying relations among genes. Although many...

    Jing Liu, Yaxiong Chi, Chen Zhu and Yaochu Jin

    BMC Bioinformatics 2017 18:241

    Published on: 8 May 2017

  8. Database

    Geminivirus data warehouse: a database enriched with machine learning approaches

    The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible fo...

    Jose Cleydson F. Silva, Thales F. M. Carvalho, Marcos F. Basso, Michihito Deguchi, Welison A. Pereira, Roberto R. Sobrinho, Pedro M. P. Vidigal, Otávio J. B. Brustolini, Fabyano F. Silva, Maximiller Dal-Bianco, Renildes L. F. Fontes, Anésia A. Santos, Francisco Murilo Zerbini, Fabio R. Cerqueira and Elizabeth P. B. Fontes

    BMC Bioinformatics 2017 18:240

    Published on: 5 May 2017

  9. Software

    microTaboo: a general and practical solution to the k-disjoint problem

    A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting....

    Mohammed Al-Jaff, Eric Sandström and Manfred Grabherr

    BMC Bioinformatics 2017 18:228

    Published on: 2 May 2017

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

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