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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. Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attr...

    Authors: Gabriela F. Rodrigues-Luiz, Mariana S. Cardoso, Hugo O. Valdivia, Edward V. Ayala, Célia M. F. Gontijo, Thiago de S. Rodrigues, Ricardo T. Fujiwara, Robson S. Lopes and Daniella C. Bartholomeu

    Citation: BMC Bioinformatics 2017 18:104

    Content type: Software

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  2. Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme e...

    Authors: Tran Tuan-Anh, Le Thi Ly, Ngo Quoc Viet and Pham The Bao

    Citation: BMC Bioinformatics 2017 18:100

    Content type: Methodology article

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  3. The correct protein coding region identification is an important and latent problem in the molecular biology field. This problem becomes a challenge due to the lack of deep knowledge about the biological syste...

    Authors: Cristiano Lacerda Nunes Pinto, Cristiane Neri Nobre and Luis Enrique Zárate

    Citation: BMC Bioinformatics 2017 18:81

    Content type: Methodology Article

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  4. The regulation of all gene expression steps (e.g., Transcription, RNA processing, Translation, and mRNA Degradation) is known to be primarily encoded in different parts of genes and in genomic regions in proxi...

    Authors: Zohar Zafrir and Tamir Tuller

    Citation: BMC Bioinformatics 2017 18:77

    Content type: Research article

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  6. Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic p...

    Authors: O. Pipek, D. Ribli, J. Molnár, Á. Póti, M. Krzystanek, A. Bodor, G. E. Tusnády, Z. Szallasi, I. Csabai and D. Szüts

    Citation: BMC Bioinformatics 2017 18:73

    Content type: Methodology article

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  7. A large amount of research has been devoted to the detection and investigation of epistatic interactions in genome-wide association studies (GWASs). Most of the literature focuses on low-order interactions bet...

    Authors: Virginie Stanislas, Cyril Dalmasso and Christophe Ambroise

    Citation: BMC Bioinformatics 2017 18:54

    Content type: Methodology Article

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  9. Next-generation sequencing of matched tumor and normal biopsy pairs has become a technology of paramount importance for precision cancer treatment. Sequencing costs have dropped tremendously, allowing the sequ...

    Authors: Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch and Niko Beerenwinkel

    Citation: BMC Bioinformatics 2017 18:8

    Content type: Research Article

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  10. Recent advances in next-generation sequencing (NGS) technology enable researchers to collect a large volume of metagenomic sequencing data. These data provide valuable resources for investigating interactions ...

    Authors: Xinyan Zhang, Himel Mallick, Zaixiang Tang, Lei Zhang, Xiangqin Cui, Andrew K. Benson and Nengjun Yi

    Citation: BMC Bioinformatics 2017 18:4

    Content type: Methodology article

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  11. A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable qu...

    Authors: Markus Lux, Jan Krüger, Christian Rinke, Irena Maus, Andreas Schlüter, Tanja Woyke, Alexander Sczyrba and Barbara Hammer

    Citation: BMC Bioinformatics 2016 17:543

    Content type: Software

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  12. Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop se...

    Authors: Amir H. Bayegan, Juan Antonio Garcia-Martin and Peter Clote

    Citation: BMC Bioinformatics 2016 17:530

    Content type: Research Article

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  13. Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedl...

    Authors: Camilo Andrés Mora Osorio and Andrés Fernando González Barrios

    Citation: BMC Bioinformatics 2016 17:522

    Content type: Research article

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  14. One of the greatest challenges in cancer genomics is to distinguish driver mutations from passenger mutations. Whereas recurrence is a hallmark of driver mutations, it is difficult to observe recurring noncodi...

    Authors: Woojin Yang, Hyoeun Bang, Kiwon Jang, Min Kyung Sung and Jung Kyoon Choi

    Citation: BMC Bioinformatics 2016 17:492

    Content type: Research article

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  15. Dicer is necessary for the process of mature microRNA (miRNA) formation because the Dicer enzyme cleaves pre-miRNA correctly to generate miRNA with correct seed regions. Nonetheless, the mechanism underlying t...

    Authors: Yu Bao, Morihiro Hayashida and Tatsuya Akutsu

    Citation: BMC Bioinformatics 2016 17:487

    Content type: Research Article

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  16. CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an ...

    Authors: Giovanni Scala, Ornella Affinito, Domenico Palumbo, Ermanno Florio, Antonella Monticelli, Gennaro Miele, Lorenzo Chiariotti and Sergio Cocozza

    Citation: BMC Bioinformatics 2016 17:484

    Content type: Software

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  19. Copy Number Variation (CNV) is envisaged to be a major source of large structural variations in the human genome. In recent years, many studies apply Next Generation Sequencing (NGS) data for the CNV detection...

    Authors: Seyed Amir Malekpour, Hamid Pezeshk and Mehdi Sadeghi

    Citation: BMC Bioinformatics 2016 18:30

    Content type: Methodology article

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  20. The problem of de-novo assembly for metagenomes using only long reads is gaining attention. We study whether post-processing metagenomic assemblies with the original input long reads can result in quality impr...

    Authors: Ka-Kit Lam, Richard Hall, Alicia Clum and Satish Rao

    Citation: BMC Bioinformatics 2016 17:435

    Content type: Research Article

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  22. T cells and B cells are essential in the adaptive immunity via expressing T cell receptors and immunoglogulins respectively for recognizing antigens. To recognize a wide variety of antigens, a highly diverse r...

    Authors: Sheng-Jou Hung, Yi-Lin Chen, Chia-Hung Chu, Chuan-Chun Lee, Wan-Li Chen, Ya-Lan Lin, Ming-Ching Lin, Chung-Liang Ho and Tsunglin Liu

    Citation: BMC Bioinformatics 2016 17:433

    Content type: Software

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  23. Multiplex polymerase chain reaction (PCR) is a common enrichment technique for targeted massive parallel sequencing (MPS) protocols. MPS is widely used in biomedical research and clinical diagnostics as the fa...

    Authors: German Demidov, Tamara Simakova, Julia Vnuchkova and Anton Bragin

    Citation: BMC Bioinformatics 2016 17:429

    Content type: Research Article

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  24. Biological sequence motifs drive the specific interactions of proteins and nucleic acids. Accordingly, the effective computational discovery and analysis of such motifs is a central theme in bioinformatics. Ma...

    Authors: Patrick K. O’Neill and Ivan Erill

    Citation: BMC Bioinformatics 2016 17:406

    Content type: Methodology Article

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  26. The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and ...

    Authors: Daniel R. Zerbino, Tracy Ballinger, Benedict Paten, Glenn Hickey and David Haussler

    Citation: BMC Bioinformatics 2016 17:400

    Content type: Methodology Article

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  28. Next-generation sequencing (NGS) has revolutionized how research is carried out in many areas of biology and medicine. However, the analysis of NGS data remains a major obstacle to the efficient utilization of...

    Authors: Tyler W. H. Backman and Thomas Girke

    Citation: BMC Bioinformatics 2016 17:388

    Content type: Software

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  29. Variations in DNA copy number have an important contribution to the development of several diseases, including autism, schizophrenia and cancer. Single-cell sequencing technology allows the dissection of genom...

    Authors: Changsheng Zhang, Hongmin Cai, Jingying Huang and Yan Song

    Citation: BMC Bioinformatics 2016 17:384

    Content type: Research Article

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  30. Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enab...

    Authors: Kiyoshi Ezawa

    Citation: BMC Bioinformatics 2016 17:304

    Content type: Research article

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    The Erratum to this article has been published in BMC Bioinformatics 2016 17:457

  31. Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-se...

    Authors: Lydia Müller, Daniel Gerighausen, Mariam Farman and Dirk Zeckzer

    Citation: BMC Bioinformatics 2016 17:377

    Content type: Methodology Article

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  33. Protein secondary structure prediction (SSP) has been an area of intense research interest. Despite advances in recent methods conducted on large datasets, the estimated upper limit accuracy is yet to be reach...

    Authors: Shamima Rashid, Saras Saraswathi, Andrzej Kloczkowski, Suresh Sundaram and Andrzej Kolinski

    Citation: BMC Bioinformatics 2016 17:362

    Content type: Methodology Article

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  34. Metaheuristics are widely used to solve large combinatorial optimization problems in bioinformatics because of the huge set of possible solutions. Two representative problems are gene selection for cancer clas...

    Authors: Juan A. Gomez-Pulido, Jose L. Cerrada-Barrios, Sebastian Trinidad-Amado, Jose M. Lanza-Gutierrez, Ramon A. Fernandez-Diaz, Broderick Crawford and Ricardo Soto

    Citation: BMC Bioinformatics 2016 17:330

    Content type: Research Article

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  36. Biological/genetic data is a complex mix of various forms or topologies which makes it quite difficult to analyze. An abundance of such data in this modern era requires the development of sophisticated statist...

    Authors: Alok Sharma, Daichi Shigemizu, Keith A. Boroevich, Yosvany López, Yoichiro Kamatani, Michiaki Kubo and Tatsuhiko Tsunoda

    Citation: BMC Bioinformatics 2016 17:319

    Content type: Research article

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  37. Reactive oxygen species can modify the structure and function of proteins and may also act as important signaling molecules in various cellular processes. Cysteine thiol groups of proteins are particularly sus...

    Authors: Ming-an Sun, Qing Zhang, Yejun Wang, Wei Ge and Dianjing Guo

    Citation: BMC Bioinformatics 2016 17:316

    Content type: Methodology article

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  38. Metagenomics holds great promises for deepening our knowledge of key bacterial driven processes, but metagenome assembly remains problematic, typically resulting in representation biases and discarding signifi...

    Authors: Anestis Gkanogiannis, Stéphane Gazut, Marcel Salanoubat, Sawsan Kanj and Thomas Brüls

    Citation: BMC Bioinformatics 2016 17:311

    Content type: Methodology article

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  39. Copy number alteration is a main genetic structural variation that plays an important role in tumor initialization and progression. Accurate detection of copy number alterations is necessary for discovering ca...

    Authors: Zhenhua Yu, Ao Li and Minghui Wang

    Citation: BMC Bioinformatics 2016 17:310

    Content type: Methodology article

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  41. DNA methylation is an important regulator of gene expression and chromatin structure. Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is commonly used to identify regions of DNA methylation in eukary...

    Authors: Umar Niazi, Kathrin K. Geyer, Martin J. Vickers, Karl F. Hoffmann and Martin T. Swain

    Citation: BMC Bioinformatics 2016 17:295

    Content type: Software

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  42. Next generation sequencing technology has enabled characterization of metagenomics through massively parallel genomic DNA sequencing. The complexity and diversity of environmental samples such as the human gut...

    Authors: Aaron Y. Lee, Cecilia S. Lee and Russell N. Van Gelder

    Citation: BMC Bioinformatics 2016 17:292

    Content type: Software

    Published on:

  43. Clustering is a common technique used by molecular biologists to group homologous sequences and study evolution. There remain issues such as how to cluster molecular sequences accurately and in particular how ...

    Authors: Shunpu Zhang, Zhong Li, Kevin Beland and Guoqing Lu

    Citation: BMC Bioinformatics 2016 17:287

    Content type: Methodology article

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  44. A standard procedure in many areas of bioinformatics is to use a multiple sequence alignment (MSA) as the basis for various types of homology-based inference. Applications include 3D structure modelling, prote...

    Authors: Renaud Vanhoutreve, Arnaud Kress, Baptiste Legrand, Hélène Gass, Olivier Poch and Julie D. Thompson

    Citation: BMC Bioinformatics 2016 17:271

    Content type: Methodology article

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  48. The growing complexity of biological experiment design based on high-throughput RNA sequencing (RNA-seq) is calling for more accommodative statistical tools. We focus on differential expression (DE) analysis u...

    Authors: Guangliang Kang, Li Du and Hong Zhang

    Citation: BMC Bioinformatics 2016 17:248

    Content type: Methodology Article

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  49. Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs....

    Authors: Antoine Limasset, Bastien Cazaux, Eric Rivals and Pierre Peterlongo

    Citation: BMC Bioinformatics 2016 17:237

    Content type: Research Article

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