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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

    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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. Content type: Methodology article

    Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar...

    Authors: Luc Villandré, Aurélie Labbe, Bluma Brenner, Michel Roger and David A Stephens

    Citation: BMC Bioinformatics 2018 19:324

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  10. Content type: Methodology article

    Normalization is essential to ensure accurate analysis and proper interpretation of sequencing data, and chromosome conformation capture data such as Hi-C have particular challenges. Although several methods h...

    Authors: Nicolas Servant, Nelle Varoquaux, Edith Heard, Emmanuel Barillot and Jean-Philippe Vert

    Citation: BMC Bioinformatics 2018 19:313

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  11. Content type: Research article

    Viral infection by dengue virus is a major public health problem in tropical countries. Early diagnosis and detection are increasingly based on quantitative reverse transcriptase real-time polymerase chain rea...

    Authors: Kevin Vanneste, Linda Garlant, Sylvia Broeders, Steven Van Gucht and Nancy H. Roosens

    Citation: BMC Bioinformatics 2018 19:312

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  12. Content type: Methodology article

    Targeted resequencing with high-throughput sequencing (HTS) platforms can be used to efficiently interrogate the genomes of large numbers of individuals. A critical issue for research and applications using HT...

    Authors: Felix Francis, Michael D. Dumas, Scott B. Davis and Randall J. Wisser

    Citation: BMC Bioinformatics 2018 19:302

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  13. Content type: Software

    Here, we present an R package for entropy/variability analysis that facilitates prompt and convenient data extraction, manipulation and visualization of protein features from multiple sequence alignments. BALC...

    Authors: Alicja Płuciennik, Michał Stolarczyk, Maria Bzówka, Agata Raczyńska, Tomasz Magdziarz and Artur Góra

    Citation: BMC Bioinformatics 2018 19:300

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  14. Content type: Software

    Taxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it’s often difficult to distinguish on morphology only. DNA barcodes allow a rapid species discove...

    Authors: Renato Renison Moreira Oliveira, Gisele Lopes Nunes, Talvâne Glauber Lopes de Lima, Guilherme Oliveira and Ronnie Alves

    Citation: BMC Bioinformatics 2018 19:297

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  15. Content type: Software

    Since circular RNAs (circRNAs) post-transcriptionally regulate gene expression, they have attracted increasing attention. However, there is no existing tool to annotate and extract spliced sequences for circRN...

    Authors: Shanliang Zhong, Jinyan Wang, Qian Zhang, Hanzi Xu and Jifeng Feng

    Citation: BMC Bioinformatics 2018 19:292

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  16. Content type: Software

    miRNAs play important roles in the regulation of gene expression. The rapidly developing field of microRNA sequencing (miRNA-seq; small RNA-seq) needs comprehensive, robust, user-friendly and standardized bioi...

    Authors: Yin Lu, Alexander S. Baras and Marc K. Halushka

    Citation: BMC Bioinformatics 2018 19:275

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  17. Content type: Methodology article

    Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation and nucleotide mutation due to their repetitive and ...

    Authors: Devika Ganesamoorthy, Minh Duc Cao, Tania Duarte, Wenhan Chen and Lachlan Coin

    Citation: BMC Bioinformatics 2018 19:267

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  18. Content type: Methodology article

    Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombinat...

    Authors: Haojing Shao, Devika Ganesamoorthy, Tania Duarte, Minh Duc Cao, Clive J. Hoggart and Lachlan J. M. Coin

    Citation: BMC Bioinformatics 2018 19:261

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  19. Content type: Methodology article

    Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each ...

    Authors: Panu Somervuo, Patrik Koskinen, Peng Mei, Liisa Holm, Petri Auvinen and Lars Paulin

    Citation: BMC Bioinformatics 2018 19:257

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  20. Content type: Methodology article

    Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays...

    Authors: Stefano Beretta, Murray D. Patterson, Simone Zaccaria, Gianluca Della Vedova and Paola Bonizzoni

    Citation: BMC Bioinformatics 2018 19:252

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  21. Content type: Software

    The advent of next-generation sequencing (NGS) has made whole-genome sequencing of cohorts of individuals a reality. Primary datasets of raw or aligned reads of this sort can get very large. For scientific que...

    Authors: Kristiina Ausmees, Aji John, Salman Z. Toor, Andreas Hellander and Carl Nettelblad

    Citation: BMC Bioinformatics 2018 19:240

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  22. Content type: Research article

    The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transpl...

    Authors: Maria Luisa Matey-Hernandez, Søren Brunak and Jose M. G. Izarzugaza

    Citation: BMC Bioinformatics 2018 19:239

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  23. Content type: Methodology article

    Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of g...

    Authors: Marcel Smid, Robert R. J. Coebergh van den Braak, Harmen J. G. van de Werken, Job van Riet, Anne van Galen, Vanja de Weerd, Michelle van der Vlugt-Daane, Sandra I. Bril, Zarina S. Lalmahomed, Wigard P. Kloosterman, Saskia M. Wilting, John A. Foekens, Jan N. M. IJzermans, John W. M. Martens and Anieta M. Sieuwerts

    Citation: BMC Bioinformatics 2018 19:236

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  24. Content type: Methodology article

    Spastic cerebral palsy (CP) is a leading cause of physical disability. Most people with spastic CP are born with it, but early diagnosis is challenging, and no current biomarker platform readily identifies aff...

    Authors: Erin L. Crowgey, Adam G. Marsh, Karyn G. Robinson, Stephanie K. Yeager and Robert E. Akins

    Citation: BMC Bioinformatics 2018 19:225

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  25. Content type: Research article

    Given a set of t n-length DNA sequences, q satisfying 0 < q ≤ 1, and l and d satisfying 0 ≤ d < l < n, the quorum planted motif search (qPMS) finds l-length strings that occur in at least qt input sequences with ...

    Authors: Qiang Yu, Dingbang Wei and Hongwei Huo

    Citation: BMC Bioinformatics 2018 19:228

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  26. Content type: Methodology article

    With the reduction of gene sequencing cost and demand for emerging technologies such as precision medical treatment and deep learning in genome, it is an era of gene data outbreaks today. How to store, transmi...

    Authors: Qiuming Luo, Chao Guo, Yi Jun Zhang, Ye Cai and Gang Liu

    Citation: BMC Bioinformatics 2018 19:230

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  27. Content type: Research article

    Third generation sequencing technologies generate long reads that exhibit high error rates, in particular for insertions and deletions which are usually the most difficult errors to cope with. The only exact a...

    Authors: Jean-François Gibrat

    Citation: BMC Bioinformatics 2018 19:226

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  28. Content type: Software

    Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by t...

    Authors: Tara N. Furstenau, Jill H. Cocking, Jason W. Sahl and Viacheslav Y. Fofanov

    Citation: BMC Bioinformatics 2018 19:222

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  29. Content type: Methodology article

    Genome annotation is of key importance in many research questions. The identification of protein-coding genes is often based on transcriptome sequencing data, ab-initio or homology-based prediction. Recently, it ...

    Authors: Jens Keilwagen, Frank Hartung, Michael Paulini, Sven O. Twardziok and Jan Grau

    Citation: BMC Bioinformatics 2018 19:189

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  30. Content type: Research article

    The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog...

    Authors: Deborah Galpert, Alberto Fernández, Francisco Herrera, Agostinho Antunes, Reinaldo Molina-Ruiz and Guillermin Agüero-Chapin

    Citation: BMC Bioinformatics 2018 19:166

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  31. Content type: Methodology article

    Activation induced deaminase (AID) and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) are deaminases that mutate C to U on single-stranded DNA (ssDNA). AID is expressed primarily ...

    Authors: Maxwell Shapiro, Stephen Meier and Thomas MacCarthy

    Citation: BMC Bioinformatics 2018 19:163

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    The Correction to this article has been published in BMC Bioinformatics 2018 19:256

  32. Content type: Software

    Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together wit...

    Authors: Jan Budczies, Nicole Pfarr, Eva Romanovsky, Volker Endris, Albrecht Stenzinger and Carsten Denkert

    Citation: BMC Bioinformatics 2018 19:157

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  33. Content type: Research article

    Detailed modelling of the neutral mutational process in cancer cells is crucial for identifying driver mutations and understanding the mutational mechanisms that act during cancer development. The neutral muta...

    Authors: Johanna Bertl, Qianyun Guo, Malene Juul, Søren Besenbacher, Morten Muhlig Nielsen, Henrik Hornshøj, Jakob Skou Pedersen and Asger Hobolth

    Citation: BMC Bioinformatics 2018 19:147

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  34. Content type: Methodology

    Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments where adjacent segments have different properties, such as different mean value...

    Authors: Senthil B. Girimurugan, Yuhang Liu, Pei-Yau Lung, Daniel L. Vera, Jonathan H. Dennis, Hank W. Bass and Jinfeng Zhang

    Citation: BMC Bioinformatics 2018 19:131

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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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