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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. Content type: Software

    Multi-label classification has recently gained great attention in diverse fields of research, e.g., in biomedical application such as protein function prediction or drug resistance testing in HIV. In this cont...

    Authors: Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch and Dominik Heider

    Citation: BMC Bioinformatics 2017 18:371

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  2. Content type: Research Article

    Drug resistance in HIV treatment is still a worldwide problem. Predicting resistance to antiretrovirals (ARVs) before starting any treatment is important. Prediction accuracy is essential, as low-accuracy pred...

    Authors: Olivier Sheik Amamuddy, Nigel T. Bishop and Özlem Tastan Bishop

    Citation: BMC Bioinformatics 2017 18:369

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  3. Content type: Software

    Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density...

    Authors: Gregory J. Zynda, Jawon Song, Lorenzo Concia, Emily E. Wear, Linda Hanley-Bowdoin, William F. Thompson and Matthew W. Vaughn

    Citation: BMC Bioinformatics 2017 18:362

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  4. Content type: Methodology Article

    Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patt...

    Authors: James E. Barrett, Andrew Feber, Javier Herrero, Miljana Tanic, Gareth A. Wilson, Charles Swanton and Stephan Beck

    Citation: BMC Bioinformatics 2017 18:354

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  5. Content type: Research article

    Large sample sets of whole genome sequencing with deep coverage are being generated, however assembling datasets from different sources inevitably introduces batch effects. These batch effects are not well und...

    Authors: Jennifer A. Tom, Jens Reeder, William F. Forrest, Robert R. Graham, Julie Hunkapiller, Timothy W. Behrens and Tushar R. Bhangale

    Citation: BMC Bioinformatics 2017 18:351

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  6. Content type: Methodology Article

    Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been s...

    Authors: Eleni Ioanna Delatola, Emilie Lebarbier, Tristan Mary-Huard, François Radvanyi, Stéphane Robin and Jennifer Wong

    Citation: BMC Bioinformatics 2017 18:333

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  7. Content type: Software

    The major histocompatibility complex (MHC) region of the human genome, and specifically the human leukocyte antigen (HLA) genes, play a major role in numerous human diseases. With the recent progress of sequen...

    Authors: Marc Jeanmougin, Josselin Noirel, Cédric Coulonges and Jean-François Zagury

    Citation: BMC Bioinformatics 2017 18:334

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  8. Content type: Methodology Article

    For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This lea...

    Authors: Axel Wedemeyer, Lasse Kliemann, Anand Srivastav, Christian Schielke, Thorsten B. Reusch and Philip Rosenstiel

    Citation: BMC Bioinformatics 2017 18:324

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  9. Content type: Software

    The identification of copy number variants (CNVs) is essential to study human genetic variation and to understand the genetic basis of mendelian disorders and cancers. At present, genome-wide detection of CNVs...

    Authors: Valerio Orlandini, Aldesia Provenzano, Sabrina Giglio and Alberto Magi

    Citation: BMC Bioinformatics 2017 18:321

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  10. Content type: Research article

    DNA-binding proteins perform important functions in a great number of biological activities. DNA-binding proteins can interact with ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA), and DNA-binding p...

    Authors: Wei Wang, Lin Sun, Shiguang Zhang, Hongjun Zhang, Jinling Shi, Tianhe Xu and Keliang Li

    Citation: BMC Bioinformatics 2017 18:300

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  11. Content type: Software

    Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipeli...

    Authors: Alex M. Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta and Marcos J. Araúzo-Bravo

    Citation: BMC Bioinformatics 2017 18:296

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  12. Content type: Research Article

    Detecting homologous protein sequences and computing multiple sequence alignments (MSA) are fundamental tasks in molecular bioinformatics. These tasks usually require a substitution matrix for modeling evoluti...

    Authors: Frank Keul, Martin Hess, Michael Goesele and Kay Hamacher

    Citation: BMC Bioinformatics 2017 18:293

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  13. Content type: Research article

    Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have creat...

    Authors: Fatima Zare, Michelle Dow, Nicholas Monteleone, Abdelrahman Hosny and Sheida Nabavi

    Citation: BMC Bioinformatics 2017 18:286

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  14. Content type: Research Article

    Microbiome studies commonly use 16S rRNA gene amplicon sequencing to characterize microbial communities. Errors introduced at multiple steps in this process can affect the interpretation of the data. Here we e...

    Authors: Jonathan L. Golob, Elisa Margolis, Noah G. Hoffman and David N. Fredricks

    Citation: BMC Bioinformatics 2017 18:283

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  15. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:270

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  16. Content type: Research Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:264

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  17. Content type: Research Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:263

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  18. Content type: Commentary

    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...

    Authors: Ian H. Holmes

    Citation: BMC Bioinformatics 2017 18:255

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  19. Content type: Methodology Article

    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, ...

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

    Citation: BMC Bioinformatics 2017 18:258

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  20. Content type: Software

    Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provid...

    Authors: Xiang Gao, Huaiying Lin, Kashi Revanna and Qunfeng Dong

    Citation: BMC Bioinformatics 2017 18:247

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  21. Content type: Research Article

    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...

    Authors: Jing Liu, Yaxiong Chi, Chen Zhu and Yaochu Jin

    Citation: BMC Bioinformatics 2017 18:241

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  22. Content type: Software

    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...

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

    Citation: BMC Bioinformatics 2017 18:242

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  23. Content type: Database

    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...

    Authors: 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

    Citation: BMC Bioinformatics 2017 18:240

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  24. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:223

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  25. Content type: Software

    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...

    Authors: Mark D. Temple

    Citation: BMC Bioinformatics 2017 18:221

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  26. Content type: Research Article

    Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While ther...

    Authors: Sarvesh Nikumbh and Nico Pfeifer

    Citation: BMC Bioinformatics 2017 18:218

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  27. Content type: Research Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:208

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  28. Content type: Research Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:210

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  29. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:199

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  30. Content type: Research article

    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...

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

    Citation: BMC Bioinformatics 2017 18:191

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

  31. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:173

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  32. Content type: Software

    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...

    Authors: Kristian Hovde Liland, Hilde Vinje and Lars Snipen

    Citation: BMC Bioinformatics 2017 18:172

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  33. Content type: Methodology Article

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

    Authors: 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

    Citation: BMC Bioinformatics 2017 18:156

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  34. Content type: Methodology article

    The B and T cells of the human adaptive immune system leverage a highly diverse repertoire of antigen-specific receptors to protect the human body from pathogens. The sequencing and analysis of immune repertoi...

    Authors: Christopher R. Bolen, Florian Rubelt, Jason A. Vander Heiden and Mark M. Davis

    Citation: BMC Bioinformatics 2017 18:155

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  35. Content type: Methodology article

    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 ...

    Authors: 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

    Citation: BMC Bioinformatics 2017 18:147

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  36. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:143

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  37. Content type: Methodology article

    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...

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

    Citation: BMC Bioinformatics 2017 18:139

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2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)


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