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Sequence analysis (applications)

Section edited by João Setubal

This section incorporates all aspects of sequence analysis applications, including but not limited to: software, workflows and webservers dealing with applied sequence/genome analysis, sequence assembly, analysis of sequence features, and protein function and ligand binding, estimated through sequence features.

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  1. A computationally efficient tool is required for a genome-wide gene-gene interaction analysis that tests an extremely large number of single-nucleotide polymorphism (SNP) interaction pairs in genome-wide assoc...

    Authors: Pei-Yuan Sung, Yi-Ting Wang, Chao A. Hsiung and Ren-Hua Chung

    Citation: BMC Bioinformatics 2016 17:273

    Content type: Software

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  2. MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6–8 nucleotide long target sites, usually located wi...

    Authors: Bridget C. Ryan, Torben S. Werner, Perry L. Howard and Robert L. Chow

    Citation: BMC Bioinformatics 2016 17:190

    Content type: Software

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  3. The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. W...

    Authors: Maude Ardin, Vincent Cahais, Xavier Castells, Liacine Bouaoun, Graham Byrnes, Zdenko Herceg, Jiri Zavadil and Magali Olivier

    Citation: BMC Bioinformatics 2016 17:170

    Content type: Software

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  4. Previously, we described ROVER, a DNA variant caller which identifies genetic variants from PCR-targeted massively parallel sequencing (MPS) datasets generated by the Hi-Plex protocol. ROVER permits stringent ...

    Authors: Daniel J. Park, Roger Li, Edmund Lau, Peter Georgeson, Tú Nguyen-Dumont and Bernard J. Pope

    Citation: BMC Bioinformatics 2016 17:165

    Content type: Software

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  5. Scaffolding is an essential step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in contiguity but often lack consistency in repetitive ...

    Authors: Mohammed-Amin Madoui, Carole Dossat, Léo d’Agata, Jan van Oeveren, Edwin van der Vossen and Jean-Marc Aury

    Citation: BMC Bioinformatics 2016 17:115

    Content type: Methodology article

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  6. The use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification. The first nanopore sequencer availab...

    Authors: Joaquin Tarraga, Asunción Gallego, Vicente Arnau, Ignacio Medina and Joaquin Dopazo

    Citation: BMC Bioinformatics 2016 17:107

    Content type: Software

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  7. The increasing availability of resequencing data has led to a better understanding of the most important genes in cancer development. Nevertheless, the mutational landscape of many tumor types is heterogeneous...

    Authors: Giorgio E. M. Melloni, Stefano de Pretis, Laura Riva, Mattia Pelizzola, Arnaud Céol, Jole Costanza, Heiko Müller and Luca Zammataro

    Citation: BMC Bioinformatics 2016 17:80

    Content type: Software

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  8. The sequencing of immunoglobulin (Ig) transcripts from single B cells yields essential information about Ig heavy:light chain pairing, which is lost in conventional bulk sequencing experiments. The previously ...

    Authors: Katharina Imkeller, Peter F. Arndt, Hedda Wardemann and Christian E. Busse

    Citation: BMC Bioinformatics 2016 17:67

    Content type: Software

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  9. The impressively low cost and improved quality of genome sequencing provides to researchers of genetic diseases, such as cancer, a powerful tool to better understand the underlying genetic mechanisms of those ...

    Authors: Christos Kozanitis and David A. Patterson

    Citation: BMC Bioinformatics 2016 17:63

    Content type: Software

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  10. Data from a plethora of high-throughput sequencing studies is readily available to researchers, providing genetic variants detected in a variety of healthy and disease populations. While each individual cohort...

    Authors: Jörg Hakenberg, Wei-Yi Cheng, Philippe Thomas, Ying-Chih Wang, Andrew V. Uzilov and Rong Chen

    Citation: BMC Bioinformatics 2016 17:24

    Content type: DATABASE

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  11. The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as un...

    Authors: Andy Kilianski, Patrick Carcel, Shijie Yao, Pierce Roth, Josh Schulte, Greg B. Donarum, Ed T. Fochler, Jessica M. Hill, Alvin T. Liem, Michael R. Wiley, Jason T. Ladner, Bradley P. Pfeffer, Oliver Elliot, Alexandra Petrosov, Dereje D. Jima, Tyghe G. Vallard…

    Citation: BMC Bioinformatics 2015 16:416

    Content type: Software

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  12. Short and long range correlations in biological sequences are central in genomic studies of covariation. These correlations can be studied using mutual information because it measures the amount of information...

    Authors: Flavio Lichtenstein, Fernando Antoneli Jr and Marcelo R. S. Briones

    Citation: BMC Bioinformatics 2015 16:409

    Content type: Software

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  13. Next generation sequencing enables studying heterogeneous populations of viral infections. When the sequencing is done at high coverage depth (“deep sequencing”), low frequency variants can be detected. Here w...

    Authors: Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie Verbist, Joke Reumers, Herman van Vlijmen and Jeroen Aerssens

    Citation: BMC Bioinformatics 2015 16:379

    Content type: Methodology article

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  14. The detection of regulatory regions in candidate sequences is essential for the understanding of the regulation of a particular gene and the mechanisms involved. This paper proposes a novel methodology based o...

    Authors: Joan Maynou, Erola Pairó, Santiago Marco and Alexandre Perera

    Citation: BMC Bioinformatics 2015 16:377

    Content type: Methodology Article

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  15. The explosion of NGS (Next Generation Sequencing) sequence data requires a huge effort in Bioinformatics methods and analyses. The creation of dedicated, robust and reliable pipelines able to handle dozens of ...

    Authors: Cécile Monat, Christine Tranchant-Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela-Bouniol, Maryline Summo and François Sabot

    Citation: BMC Bioinformatics 2015 16:374

    Content type: SOFTWARE

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  16. MicroRNAs (miRNAs) are short regulatory RNAs derived from longer precursor RNAs. miRNA biogenesis has been studied in animals and plants, recently elucidating more complex aspects, such as non-conserved, speci...

    Authors: Maurits Evers, Michael Huttner, Anne Dueck, Gunter Meister and Julia C. Engelmann

    Citation: BMC Bioinformatics 2015 16:370

    Content type: Software

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  17. Recently, rapid improvements in technology and decrease in sequencing costs have made RNA-Seq a widely used technique to quantify gene expression levels. Various normalization approaches have been proposed, ow...

    Authors: Peipei Li, Yongjun Piao, Ho Sun Shon and Keun Ho Ryu

    Citation: BMC Bioinformatics 2015 16:347

    Content type: Research article

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  18. One of the most important somatic aberrations, copy number variations (CNVs) in tumor genomes is believed to have a high probability of harboring oncotargets. Detection of somatic CNVs is an essential part of ...

    Authors: Lingnan Ma, Maochun Qin, Biao Liu, Qiang Hu, Lei Wei, Jianmin Wang and Song Liu

    Citation: BMC Bioinformatics 2015 16:331

    Content type: Software

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  19. Copy number variations are important in the detection and progression of significant tumors and diseases. Recently, Whole Exome Sequencing is gaining popularity with copy number variations detection due to low...

    Authors: Samreen Anjum, Sandro Morganella, Fulvio D’Angelo, Antonio Iavarone and Michele Ceccarelli

    Citation: BMC Bioinformatics 2015 16:315

    Content type: Methodology Article

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  20. Numerous methods are available to profile several epigenetic marks, providing data with different genome coverage and resolution. Large epigenomic datasets are then generated, and often combined with other hig...

    Authors: Kamal Kishore, Stefano de Pretis, Ryan Lister, Marco J. Morelli, Valerio Bianchi, Bruno Amati, Joseph R. Ecker and Mattia Pelizzola

    Citation: BMC Bioinformatics 2015 16:313

    Content type: Software

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  21. Next-generation sequencing (NGS) technologies have become much more efficient, allowing whole human genomes to be sequenced faster and cheaper than ever before. However, processing the raw sequence reads assoc...

    Authors: Kristopher A. Standish, Tristan M. Carland, Glenn K. Lockwood, Wayne Pfeiffer, Mahidhar Tatineni, C Chris Huang, Sarah Lamberth, Yauheniya Cherkas, Carrie Brodmerkel, Ed Jaeger, Lance Smith, Gunaretnam Rajagopal, Mark E. Curran and Nicholas J. Schork

    Citation: BMC Bioinformatics 2015 16:304

    Content type: Methodology Article

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  22. Technological advances have enabled the analysis of very small amounts of DNA in forensic cases. However, the DNA profiles from such evidence are frequently incomplete and can contain contributions from multip...

    Authors: Keith Inman, Norah Rudin, Ken Cheng, Chris Robinson, Adam Kirschner, Luke Inman-Semerau and Kirk E. Lohmueller

    Citation: BMC Bioinformatics 2015 16:298

    Content type: Software

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  23. Next-generation sequencing (NGS) has greatly facilitated metagenomic analysis but also raised new challenges for metagenomic DNA sequence assembly, owing to its high-throughput nature and extremely short reads...

    Authors: Binbin Lai, Fumeng Wang, Xiaoqi Wang, Liping Duan and Huaiqiu Zhu

    Citation: BMC Bioinformatics 2015 16:244

    Content type: Software

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  24. While next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains a significant bioinformatics challenge, es...

    Authors: Daniel Paulino, René L. Warren, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman and Inanç Birol

    Citation: BMC Bioinformatics 2015 16:230

    Content type: Software

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  25. The polymerase chain reaction (PCR) is the current state of the art technique for DNA-based detection of Genetically Modified Organisms (GMOs). A typical control strategy starts by analyzing a sample for the p...

    Authors: Alexandre Angers-Loustau, Mauro Petrillo, Laura Bonfini, Francesco Gatto, Sabrina Rosa, Alexandre Patak and Joachim Kreysa

    Citation: BMC Bioinformatics 2014 15:417

    Content type: Database

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  26. Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide ...

    Authors: Isaak Y Tecle, Jeremy D Edwards, Naama Menda, Chiedozie Egesi, Ismail Y Rabbi, Peter Kulakow, Robert Kawuki, Jean-Luc Jannink and Lukas A Mueller

    Citation: BMC Bioinformatics 2014 15:398

    Content type: Software

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  27. Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue ty...

    Authors: Antonio Fabio Di Narzo, Haoxiang Cheng, Jianwei Lu and Ke Hao

    Citation: BMC Bioinformatics 2014 15:392

    Content type: Software

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  28. High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultane...

    Authors: Thorfinn Sand Korneliussen, Anders Albrechtsen and Rasmus Nielsen

    Citation: BMC Bioinformatics 2014 15:356

    Content type: Software

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  29. With the advance of next generation sequencing (NGS) technologies, a large number of insertion and deletion (indel) variants have been identified in human populations. Despite much research into variant callin...

    Authors: Zhiyi Li, Xiaowei Wu, Bin He and Liqing Zhang

    Citation: BMC Bioinformatics 2014 15:359

    Content type: Research article

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  30. Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and meta...

    Authors: Jamison M McCorrison, Pratap Venepally, Indresh Singh, Derrick E Fouts, Roger S Lasken and Barbara A Methé

    Citation: BMC Bioinformatics 2014 15:357

    Content type: Software

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  31. Terminal restriction fragment length polymorphism (T-RFLP) analysis is a DNA-fingerprinting method that can be used for comparisons of the microbial community composition in a large number of samples. There is...

    Authors: Nils Johan Fredriksson, Malte Hermansson and Britt-Marie Wilén

    Citation: BMC Bioinformatics 2014 15:361

    Content type: Software

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  32. Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common DNA-fingerprinting technique used for comparisons of complex microbial communities. Although the technique is well established th...

    Authors: Nils Johan Fredriksson, Malte Hermansson and Britt-Marie Wilén

    Citation: BMC Bioinformatics 2014 15:360

    Content type: Methodology article

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  33. DNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation...

    Authors: Devon Patrick Ryan and Dan Ehninger

    Citation: BMC Bioinformatics 2014 15:337

    Content type: Software

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  34. Exome sequencing allows researchers to study the human genome in unprecedented detail. Among the many types of variants detectable through exome sequencing, one of the most over looked types of mutation is int...

    Authors: Yan Guo, Shilin Zhao, Brian D Lehmann, Quanhu Sheng, Timothy M Shaver, Thomas P Stricker, Jennifer A Pietenpol and Yu Shyr

    Citation: BMC Bioinformatics 2014 15:332

    Content type: Software

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  35. Quantification of a transcriptional profile is a useful way to evaluate the activity of a cell at a given point in time. Although RNA-Seq has revolutionized transcriptional profiling, the costs of RNA-Seq are ...

    Authors: Gabriel Renaud, Matthew C LaFave, Jin Liang, Tyra G Wolfsberg and Shawn M Burgess

    Citation: BMC Bioinformatics 2014 15:329

    Content type: Software

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  36. In past number of methods have been developed for predicting post-translational modifications in proteins. In contrast, limited attempt has been made to understand post-transcriptional modifications. Recently ...

    Authors: Bharat Panwar and Gajendra PS Raghava

    Citation: BMC Bioinformatics 2014 15:326

    Content type: Research article

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  37. De novo genome assembly of next-generation sequencing data is one of the most important current problems in bioinformatics, essential in many biological applications. In spite of significant amount of work in ...

    Authors: Lucian Ilie, Bahlul Haider, Michael Molnar and Roberto Solis-Oba

    Citation: BMC Bioinformatics 2014 15:302

    Content type: Software

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