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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: Methodology article

    Understanding the phenotypic drug response on cancer cell lines plays a vital role in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data ...

    Authors: Pengfei Liu, Hongjian Li, Shuai Li and Kwong-Sak Leung

    Citation: BMC Bioinformatics 2019 20:408

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  2. Content type: Software

    Human papillomavirus (HPV) is a common sexually transmitted infection associated with cervical cancer that frequently occurs as a coinfection of types and subtypes. Highly similar sublineages that show over 10...

    Authors: Eric T. Dawson, Sarah Wagner, David Roberson, Meredith Yeager, Joseph Boland, Erik Garrison, Stephen Chanock, Mark Schiffman, Tina Raine-Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello and Richard Durbin

    Citation: BMC Bioinformatics 2019 20:389

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  3. Content type: Methodology article

    Testing model adequacy is important before a DNA substitution model is chosen for phylogenetic inference. Using a mis-specified model can negatively impact phylogenetic inference, for example, the maximum like...

    Authors: Wei Chen, Toby Kenney, Joseph Bielawski and Hong Gu

    Citation: BMC Bioinformatics 2019 20:349

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  4. Content type: Software

    Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. However, until now, software that can efficiently mak...

    Authors: Xiaoshuang Liu, Zhenhe Yan, Chao Wu, Yang Yang, Xiaomin Li and Guangxin Zhang

    Citation: BMC Bioinformatics 2019 20:345

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  5. Content type: Methodology article

    Establishment of telomere maintenance mechanisms is a universal step in tumor development to achieve replicative immortality. These processes leave molecular footprints in cancer genomes in the form of altered...

    Authors: Lars Feuerbach, Lina Sieverling, Katharina I. Deeg, Philip Ginsbach, Barbara Hutter, Ivo Buchhalter, Paul A. Northcott, Sadaf S. Mughal, Priya Chudasama, Hanno Glimm, Claudia Scholl, Peter Lichter, Stefan Fröhling, Stefan M. Pfister, David T. W. Jones, Karsten Rippe…

    Citation: BMC Bioinformatics 2019 20:272

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  6. Content type: Methodology article

    In standard high throughput sequencing analysis, genetic variants are not assigned to a homologous chromosome of origin. This process, called haplotype phasing, can reveal information important for understandi...

    Authors: Alexandra R. Buckley, Trey Ideker, Hannah Carter and Nicholas J. Schork

    Citation: BMC Bioinformatics 2019 20:265

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  7. Content type: Methodology article

    Pairwise alignment of short DNA sequences with affine-gap scoring is a common processing step performed in a range of bioinformatics analyses. Dynamic programming (i.e. Smith-Waterman algorithm) is widely used...

    Authors: Arash Bayat, Bruno Gaëta, Aleksandar Ignjatovic and Sri Parameswaran

    Citation: BMC Bioinformatics 2019 20:261

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  8. Content type: Research article

    Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and interpretati...

    Authors: Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres and Philipp Rescheneder

    Citation: BMC Bioinformatics 2019 20:258

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  9. Content type: Software

    Next-generation sequencing is revolutionising diagnosis and treatment of rare diseases, however its application to understanding common disease aetiology is limited. Rare disease applications binarily attribut...

    Authors: E. Mossotto, J. J. Ashton, L. O’Gorman, R. J. Pengelly, R. M. Beattie, B. D. MacArthur and S. Ennis

    Citation: BMC Bioinformatics 2019 20:254

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  10. Content type: Methodology article

    The development of whole genome bisulfite sequencing has made it possible to identify methylation differences at single base resolution throughout an entire genome. However, a persistent challenge in DNA methy...

    Authors: Akanksha Srivastava, Yuliya V. Karpievitch, Steven R. Eichten, Justin O. Borevitz and Ryan Lister

    Citation: BMC Bioinformatics 2019 20:253

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  11. Content type: Software

    With the widespread use of multiple amplicon-sequencing (MAS) in genetic variation detection, an efficient tool is required to remove primer sequences from short reads to ensure the reliability of downstream a...

    Authors: Xiaolong Zhang, Yanyan Shao, Jichao Tian, Yuwei Liao, Peiying Li, Yu Zhang, Jun Chen and Zhiguang Li

    Citation: BMC Bioinformatics 2019 20:236

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  12. Content type: Software

    The Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.

    Authors: Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José L. Roda-García, Carlos J. Pérez-González, Marcos Colebrook and Carlos Flores

    Citation: BMC Bioinformatics 2019 20:234

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  13. Content type: Methodology article

    Draft quality genomes for a multitude of organisms have become common due to the advancement of genome assemblers using long-read technologies with high error rates. Although current assemblies are substantial...

    Authors: Philipp Bongartz

    Citation: BMC Bioinformatics 2019 20:232

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  14. Content type: Software

    RNA sequencing (RNA-seq) has become the standard means of analyzing gene and transcript expression in high-throughput. While previously sequence alignment was a time demanding step, fast alignment methods and ...

    Authors: Paula Pérez-Rubio, Claudio Lottaz and Julia C. Engelmann

    Citation: BMC Bioinformatics 2019 20:226

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  15. Content type: Methodology article

    Data from genome-wide association studies (GWASs) have been used to estimate the heritability of human complex traits in recent years. Existing methods are based on the linear mixed model, with the assumption ...

    Authors: Xin Li, Dongya Wu, Yue Cui, Bing Liu, Henrik Walter, Gunter Schumann, Chong Li and Tianzi Jiang

    Citation: BMC Bioinformatics 2019 20:219

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  16. Content type: Methodology article

    Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant chal...

    Authors: A. Iacoangeli, A. Al Khleifat, W. Sproviero, A. Shatunov, A. R. Jones, S. L. Morgan, A. Pittman, R. J. Dobson, S. J. Newhouse and A. Al-Chalabi

    Citation: BMC Bioinformatics 2019 20:213

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  17. Content type: Methodology article

    Establishment and maintenance of DNA methylation throughout the genome is an important epigenetic mechanism that regulates gene expression whose disruption has been implicated in human diseases like cancer. It...

    Authors: Garrett Jenkinson, Jordi Abante, Michael A. Koldobskiy, Andrew P. Feinberg and John Goutsias

    Citation: BMC Bioinformatics 2019 20:175

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  18. Content type: Methodology article

    Identifying transcriptional enhancers and other cis-regulatory modules (CRMs) is an important goal of post-sequencing genome annotation. Computational approaches provide a useful complement to empirical methods f...

    Authors: Hasiba Asma and Marc S. Halfon

    Citation: BMC Bioinformatics 2019 20:174

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  19. Content type: Methodology article

    Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well...

    Authors: Yu Xu, Zhe Lin, Chong Tang, Yujing Tang, Yue Cai, Hongbin Zhong, Xuebin Wang, Wenwei Zhang, Chongjun Xu, Jingjing Wang, Jian Wang, Huanming Yang, Linfeng Yang and Qiang Gao

    Citation: BMC Bioinformatics 2019 20:153

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  20. Content type: Methodology article

    Functional antibody genes are often assembled by VDJ recombination and then diversified by somatic hypermutation. Identifying the combination of sourcing germline genes is critical to understand the process of...

    Authors: Qingchen Zhang, Lu Zhang, Chen Zhou, Yiyan Yang, Zuojing Yin, Dingfeng Wu, Kailin Tang and Zhiwei Cao

    Citation: BMC Bioinformatics 2019 20:137

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  21. Content type: Research article

    As an important type of post-translational modification (PTM), protein glycosylation plays a crucial role in protein stability and protein function. The abundance and ubiquity of protein glycosylation across t...

    Authors: Fuyi Li, Yang Zhang, Anthony W. Purcell, Geoffrey I. Webb, Kuo-Chen Chou, Trevor Lithgow, Chen Li and Jiangning Song

    Citation: BMC Bioinformatics 2019 20:112

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  22. Content type: Methodology article

    Group structures among genes encoded in functional relationships or biological pathways are valuable and unique features in large-scale molecular data for survival analysis. However, most of previous approache...

    Authors: Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen and Nengjun Yi

    Citation: BMC Bioinformatics 2019 20:94

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  23. Content type: Research article

    The development of sequencing techniques and statistical methods provides great opportunities for identifying the impact of rare genetic variation on complex traits. However, there is a lack of knowledge on th...

    Authors: Xinyuan Zhang, Anna O. Basile, Sarah A. Pendergrass and Marylyn D. Ritchie

    Citation: BMC Bioinformatics 2019 20:46

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  24. Content type: Research article

    The analysis of single-cell RNA sequencing (scRNAseq) data plays an important role in understanding the intrinsic and extrinsic cellular processes in biological and biomedical research. One significant effort ...

    Authors: Tianyu Wang, Boyang Li, Craig E. Nelson and Sheida Nabavi

    Citation: BMC Bioinformatics 2019 20:40

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  25. Content type: Software

    Single-cell sequencing experiments use short DNA barcode ‘tags’ to identify reads that originate from the same cell. In order to recover single-cell information from such experiments, reads must be grouped bas...

    Authors: Akshay Tambe and Lior Pachter

    Citation: BMC Bioinformatics 2019 20:32

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  26. Content type: Methodology article

    Skewed X chromosome inactivation (XCI), which is a non-random process, is frequently observed in both healthy and affected females. Furthermore, skewed XCI has been reported to be related to many X-linked dise...

    Authors: Peng Wang, Yu Zhang, Bei-Qi Wang, Jian-Long Li, Yi-Xin Wang, Dongdong Pan, Xian-Bo Wu, Wing Kam Fung and Ji-Yuan Zhou

    Citation: BMC Bioinformatics 2019 20:11

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  27. Content type: Methodology article

    DNA methylation of CpG dinucleotides is an essential epigenetic modification that plays a key role in transcription. Widely used DNA enrichment-based methods offer high coverage for measuring methylated CpG di...

    Authors: Jingting Xu, Shimeng Liu, Ping Yin, Serdar Bulun and Yang Dai

    Citation: BMC Bioinformatics 2018 19:540

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  28. Content type: Research article

    The deployment of Genome-wide association studies (GWASs) requires genomic information of a large population to produce reliable results. This raises significant privacy concerns, making people hesitate to con...

    Authors: Charlotte Bonte, Eleftheria Makri, Amin Ardeshirdavani, Jaak Simm, Yves Moreau and Frederik Vercauteren

    Citation: BMC Bioinformatics 2018 19:537

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  29. Content type: Methodology article

    Researchers typically sequence a given individual multiple times, either re-sequencing the same DNA sample (technical replication) or sequencing different DNA samples collected on the same individual (biologic...

    Authors: Ariel W. Chan, Amy L. Williams and Jean-Luc Jannink

    Citation: BMC Bioinformatics 2018 19:478

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  30. Content type: Software

    Targeted resequencing has become the most used and cost-effective approach for identifying causative mutations of Mendelian diseases both for diagnostics and research purposes. Due to very rapid technological ...

    Authors: F. Musacchia, A. Ciolfi, M. Mutarelli, A. Bruselles, R. Castello, M. Pinelli, S. Basu, S. Banfi, G. Casari, M. Tartaglia and V. Nigro

    Citation: BMC Bioinformatics 2018 19:477

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  31. Content type: Software

    Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles...

    Authors: Roelof J. C. Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji-Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper…

    Citation: BMC Bioinformatics 2018 19:366

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  32. Content type: Research article

    Conventional methods of motor imagery brain computer interfaces (MI-BCIs) suffer from the limited number of samples and simplified features, so as to produce poor performances with spatial-frequency features a...

    Authors: Tian-jian Luo, Chang-le Zhou and Fei Chao

    Citation: BMC Bioinformatics 2018 19:344

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  33. Content type: Methodology article

    Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. The accuracy of this approach strongly depends on the choice of primer pairs and, in particu...

    Authors: Francesco Sambo, Francesca Finotello, Enrico Lavezzo, Giacomo Baruzzo, Giulia Masi, Elektra Peta, Marco Falda, Stefano Toppo, Luisa Barzon and Barbara Di Camillo

    Citation: BMC Bioinformatics 2018 19:343

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  34. Content type: Methodology article

    Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to b...

    Authors: Siavash Sheikhizadeh Anari, Dick de Ridder, M. Eric Schranz and Sandra Smit

    Citation: BMC Bioinformatics 2018 19:340

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  35. Content type: Research article

    Detection of highly divergent or yet unknown viruses from metagenomics sequencing datasets is a major bioinformatics challenge. When human samples are sequenced, a large proportion of assembled contigs are cla...

    Authors: Zurab Bzhalava, Ardi Tampuu, Piotr Bała, Raul Vicente and Joakim Dillner

    Citation: BMC Bioinformatics 2018 19:336

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  36. Content type: Methodology article

    The development of a disease is a complex process that may result from joint effects of multiple genes. In this article, we propose the overlapping group screening (OGS) approach to determining active genes an...

    Authors: Jie-Huei Wang and Yi-Hau Chen

    Citation: BMC Bioinformatics 2018 19:335

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  37. Content type: Software

    The automated prediction of the enzymatic functions of uncharacterized proteins is a crucial topic in bioinformatics. Although several methods and tools have been proposed to classify enzymes, most of these st...

    Authors: Alperen Dalkiran, Ahmet Sureyya Rifaioglu, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay and Tunca Doğan

    Citation: BMC Bioinformatics 2018 19:334

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  38. Content type: Methodology article

    Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of p...

    Authors: Massimo Maiolo, Xiaolei Zhang, Manuel Gil and Maria Anisimova

    Citation: BMC Bioinformatics 2018 19:331

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2018 Journal Metrics

  • Citation Impact
    2.511 - 2-year Impact Factor
    2.970 - 5-year Impact Factor
    0.855 - Source Normalized Impact per Paper (SNIP)
    1.374 - SCImago Journal Rank (SJR)


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