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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. Machine learning techniques are known to be a powerful way of distinguishing microRNA hairpins from pseudo hairpins and have been applied in a number of recognised miRNA search tools. However, many current met...

    Authors: Adam Gudyś, Michał Wojciech Szcześniak, Marek Sikora and Izabela Makałowska

    Citation: BMC Bioinformatics 2013 14:83

    Content type: Methodology article

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  2. Culture-independent phylogenetic analysis of 16S ribosomal RNA (rRNA) gene sequences has emerged as an incisive method of profiling bacteria present in a specimen. Currently, multiple techniques are available ...

    Authors: Xiao Wu, Kathryn Berkow, Daniel N Frank, Ellen Li, Ajay S Gulati and Wei Zhu

    Citation: BMC Bioinformatics 2013 14:79

    Content type: Research article

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  3. In methylome-wide association studies (MWAS) there are many possible differences between cases and controls (e.g. related to life style, diet, and medication use) that may affect the methylome and produce fals...

    Authors: Wenan Chen, Guimin Gao, Srilaxmi Nerella, Christina M Hultman, Patrik KE Magnusson, Patrick F Sullivan, Karolina A Aberg and Edwin JCG van den Oord

    Citation: BMC Bioinformatics 2013 14:74

    Content type: Software

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  4. DNA microarrays have become ubiquitous in biological and medical research. The most difficult problem that needs to be solved is the design of DNA oligonucleotides that (i) are highly specific, that is, bind o...

    Authors: Lucian Ilie, Hamid Mohamadi, Geoffrey Brian Golding and William F Smyth

    Citation: BMC Bioinformatics 2013 14:69

    Content type: Research article

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  5. A popular objective of many high-throughput genome projects is to discover various genomic markers associated with traits and develop statistical models to predict traits of future patients based on marker val...

    Authors: Jinseog Kim, Insuk Sohn, Dae-Soon Son, Dong Hwan Kim, Taejin Ahn and Sin-Ho Jung

    Citation: BMC Bioinformatics 2013 14:58

    Content type: Methodology article

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  6. Methylation studies are a promising complement to genetic studies of DNA sequence. However, detailed prior biological knowledge is typically lacking, so methylome-wide association studies (MWAS) will be critic...

    Authors: Edwin JCG van den Oord, Jozsef Bukszar, Gábor Rudolf, Srilaxmi Nerella, Joseph L McClay, Lin Y Xie and Karolina A Aberg

    Citation: BMC Bioinformatics 2013 14:50

    Content type: Methodology article

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  7. RNA-Seq has the potential to answer many diverse and interesting questions about the inner workings of cells. Estimating changes in the overall transcription of a gene is not straightforward. Changes in overal...

    Authors: Ellis Patrick, Michael Buckley and Yee Hwa Yang

    Citation: BMC Bioinformatics 2013 14:31

    Content type: Methodology article

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  8. Population inference is an important problem in genetics used to remove population stratification in genome-wide association studies and to detect migration patterns or shared ancestry. An individual’s genotyp...

    Authors: R Mitchell Parry and May D Wang

    Citation: BMC Bioinformatics 2013 14:28

    Content type: Research article

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  9. Identification of cis- and trans-acting factors regulating gene expression remains an important problem in biology. Bioinformatics analyses of regulatory regions are hampered by several difficulties. One is that ...

    Authors: Alexis Vandenbon, Yutaro Kumagai, Shunsuke Teraguchi, Karlou Mar Amada, Shizuo Akira and Daron M Standley

    Citation: BMC Bioinformatics 2013 14:26

    Content type: Methodology article

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  10. Multivariate approaches have been successfully applied to genome wide association studies. Recently, a Partial Least Squares (PLS) based approach was introduced for mapping yeast genotype-phenotype relations, ...

    Authors: Tahir Mehmood, Jonas Warringer, Lars Snipen and Solve Sæbø

    Citation: BMC Bioinformatics 2012 13:327

    Content type: Research article

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  11. Discovery of functionally significant short, statistically overrepresented subsequence patterns (motifs) in a set of sequences is a challenging problem in bioinformatics. Oftentimes, not all sequences in the s...

    Authors: Phillip Seitzer, Elizabeth G Wilbanks, David J Larsen and Marc T Facciotti

    Citation: BMC Bioinformatics 2012 13:317

    Content type: Research article

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  12. DNA capture technologies combined with high-throughput sequencing now enable cost-effective, deep-coverage, targeted sequencing of complete exomes. This is well suited for SNP discovery and genotyping. However...

    Authors: Jiantao Wu, Krzysztof R Grzeda, Chip Stewart, Fabian Grubert, Alexander E Urban, Michael P Snyder and Gabor T Marth

    Citation: BMC Bioinformatics 2012 13:305

    Content type: Methodology article

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  13. 454 pyrosequencing is a commonly used massively parallel DNA sequencing technology with a wide variety of application fields such as epigenetics, metagenomics and transcriptomics. A well-known problem of this ...

    Authors: Kristof De Beuf, Joachim De Schrijver, Olivier Thas, Wim Van Criekinge, Rafael A Irizarry and Lieven Clement

    Citation: BMC Bioinformatics 2012 13:303

    Content type: Methodology article

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  14. Even though the classification of cancer tissue samples based on gene expression data has advanced considerably in recent years, it faces great challenges to improve accuracy. One of the challenges is to estab...

    Authors: Hongyan Zhang, Haiyan Wang, Zhijun Dai, Ming-shun Chen and Zheming Yuan

    Citation: BMC Bioinformatics 2012 13:298

    Content type: Methodology article

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  15. Despite significant advancement in alignment algorithms, the exponential growth of nucleotide sequencing throughput threatens to outpace bioinformatic analysis. Computation may become the bottleneck of genome ...

    Authors: Brendan A Veeneman, Matthew K Iyer and Arul M Chinnaiyan

    Citation: BMC Bioinformatics 2012 13:297

    Content type: Software

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  16. Identification of causal SNPs in most genome wide association studies relies on approaches that consider each SNP individually. However, there is a strong correlation structure among SNPs that needs to be take...

    Authors: Verena Zuber, A Pedro Duarte Silva and Korbinian Strimmer

    Citation: BMC Bioinformatics 2012 13:284

    Content type: Methodology article

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  17. Structural variations (SVs) in genomes are commonly observed even in healthy individuals and play key roles in biological functions. To understand their functional impact or to infer molecular mechanisms of SV...

    Authors: Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki and Satoru Miyano

    Citation: BMC Bioinformatics 2012 13:279

    Content type: Methodology article

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  18. Despite our increasing recognition of the mechanisms that specify and propagate epigenetic states of gene expression, the pattern of how epigenetic modifications contribute to the overall genetic variation of ...

    Authors: Zhong Wang, Zuoheng Wang, Jianxin Wang, Yihan Sui, Jian Zhang, Duanping Liao and Rongling Wu

    Citation: BMC Bioinformatics 2012 13:274

    Content type: Methodology article

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  19. Performing high throughput sequencing on samples pooled from different individuals is a strategy to characterize genetic variability at a small fraction of the cost required for individual sequencing. In certa...

    Authors: Emanuele Raineri, Luca Ferretti, Anna Esteve-Codina, Bruno Nevado, Simon Heath and Miguel Pérez-Enciso

    Citation: BMC Bioinformatics 2012 13:239

    Content type: Methodology article

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  20. Recent methods have been developed to perform high-throughput sequencing of DNA by Single Molecule Sequencing (SMS). While Next-Generation sequencing methods may produce reads up to several hundred bases long,...

    Authors: Mark J Chaisson and Glenn Tesler

    Citation: BMC Bioinformatics 2012 13:238

    Content type: Methodology article

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  21. A large panel of methods exists that aim to identify residues with critical impact on protein function based on evolutionary signals, sequence and structure information. However, it is not clear to what extent...

    Authors: Elin Teppa, Angela D Wilkins, Morten Nielsen and Cristina Marino Buslje

    Citation: BMC Bioinformatics 2012 13:235

    Content type: Research article

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  22. The detection of significant compensatory mutation signals in multiple sequence alignments (MSAs) is often complicated by noise. A challenging problem in bioinformatics is remains the separation of significant...

    Authors: Mehmet Gültas, Martin Haubrock, Nesrin Tüysüz and Stephan Waack

    Citation: BMC Bioinformatics 2012 13:225

    Content type: Methodology article

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  23. The MapReduce framework enables a scalable processing and analyzing of large datasets by distributing the computational load on connected computer nodes, referred to as a cluster. In Bioinformatics, MapReduce ...

    Authors: Sebastian Schönherr, Lukas Forer, Hansi Weißensteiner, Florian Kronenberg, Günther Specht and Anita Kloss-Brandstätter

    Citation: BMC Bioinformatics 2012 13:200

    Content type: Software

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  24. Short-read data from next-generation sequencing technologies are now being generated across a range of research projects. The fidelity of this data can be affected by several factors and it is important to hav...

    Authors: Xin Victoria Wang, Natalie Blades, Jie Ding, Razvan Sultana and Giovanni Parmigiani

    Citation: BMC Bioinformatics 2012 13:185

    Content type: Methodology article

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  25. Gene prediction algorithms (or gene callers) are an essential tool for analyzing shotgun nucleic acid sequence data. Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume o...

    Authors: William L Trimble, Kevin P Keegan, Mark D’Souza, Andreas Wilke, Jared Wilkening, Jack Gilbert and Folker Meyer

    Citation: BMC Bioinformatics 2012 13:183

    Content type: Research article

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  26. Clustering DNA sequences into functional groups is an important problem in bioinformatics. We propose a new alignment-free algorithm, mBKM, based on a new distance measure, DMk, for clustering gene sequences. ...

    Authors: Dan Wei, Qingshan Jiang, Yanjie Wei and Shengrui Wang

    Citation: BMC Bioinformatics 2012 13:174

    Content type: Methodology article

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  27. The NCBI Conserved Domain Database (CDD) consists of a collection of multiple sequence alignments of protein domains that are at various stages of being manually curated into evolutionary hierarchies based on ...

    Authors: Andrew F Neuwald, Christopher J Lanczycki and Aron Marchler-Bauer

    Citation: BMC Bioinformatics 2012 13:144

    Content type: Methodology article

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  28. Computing of sequence similarity results is becoming a limiting factor in metagenome analysis. Sequence similarity search results encoded in an open, exchangeable format have the potential to limit the needs f...

    Authors: Andreas Wilke, Travis Harrison, Jared Wilkening, Dawn Field, Elizabeth M Glass, Nikos Kyrpides, Konstantinos Mavrommatis and Folker Meyer

    Citation: BMC Bioinformatics 2012 13:141

    Content type: Database

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  29. The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA) is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exha...

    Authors: Alfred Kick, Martin Bönsch and Michael Mertig

    Citation: BMC Bioinformatics 2012 13:138

    Content type: Software

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  30. The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of po...

    Authors: Peter W Collingridge and Steven Kelly

    Citation: BMC Bioinformatics 2012 13:117

    Content type: Methodology article

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  31. As Next-Generation Sequencing data becomes available, existing hardware environments do not provide sufficient storage space and computational power to store and process the data due to their enormous size. Th...

    Authors: Dandi Qiao, Wai-Ki Yip and Christoph Lange

    Citation: BMC Bioinformatics 2012 13:100

    Content type: Methodology article

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  32. A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottle...

    Authors: Konstantinos Krampis, Tim Booth, Brad Chapman, Bela Tiwari, Mesude Bicak, Dawn Field and Karen E Nelson

    Citation: BMC Bioinformatics 2012 13:42

    Content type: Software

    Published on:

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