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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. Content type: Software

    Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has ...

    Authors: Duo Xu, Yousef Jaber, Pavlos Pavlidis and Omer Gokcumen

    Citation: BMC Bioinformatics 2017 18:426

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  2. Content type: Software

    The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the u...

    Authors: José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves, Pablo Marín-Garcia, Ignacio Medina, Vicente Arnau and Joaquín Dopazo

    Citation: BMC Bioinformatics 2017 18:421

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  3. Content type: Research Article

    Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition of lymphocyte populations. This opens the door for novel approaches to diagnose and pro...

    Authors: Jared Ostmeyer, Scott Christley, William H. Rounds, Inimary Toby, Benjamin M. Greenberg, Nancy L. Monson and Lindsay G. Cowell

    Citation: BMC Bioinformatics 2017 18:401

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  4. Content type: Database

    Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codo...

    Authors: John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V. Santana-Quintero, Upendra Katneni, Vahan Simonyan and Chava Kimchi-Sarfaty

    Citation: BMC Bioinformatics 2017 18:391

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  5. Content type: Research Article

    Discriminating driver mutations from the ones that play no role in cancer is a severe bottleneck in elucidating molecular mechanisms underlying cancer development. Since protein domains are representatives of ...

    Authors: Seirana Hashemi, Abbas Nowzari Dalini, Adrin Jalali, Ali Mohammad Banaei-Moghaddam and Zahra Razaghi-Moghadam

    Citation: BMC Bioinformatics 2017 18:370

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  6. Content type: Software

    Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS...

    Authors: Carlos Guzman and Iván D’Orso

    Citation: BMC Bioinformatics 2017 18:363

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  7. Content type: Research Article

    Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in vario...

    Authors: Sheng Liu, Cristina Zibetti, Jun Wan, Guohua Wang, Seth Blackshaw and Jiang Qian

    Citation: BMC Bioinformatics 2017 18:355

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  8. Content type: Software

    In mediation analysis if unmeasured confounding is present, the estimates for the direct and mediated effects may be over or under estimated. Most methods for the sensitivity analysis of unmeasured confounding...

    Authors: Sharon M. Lutz, Annie Thwing, Sarah Schmiege, Miranda Kroehl, Christopher D. Baker, Anne P. Starling, John E. Hokanson and Debashis Ghosh

    Citation: BMC Bioinformatics 2017 18:344

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  9. Content type: Software

    The increasing volume and complexity of high-throughput genomic data make analysis and prioritization of variants difficult for researchers with limited bioinformatics skills. Variant Ranker allows researchers to...

    Authors: John Alexander, Dimitris Mantzaris, Marianthi Georgitsi, Petros Drineas and Peristera Paschou

    Citation: BMC Bioinformatics 2017 18:341

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  10. Content type: Software

    Comparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to a reference genome, or two genomes to each other. The purpose of the comparison is u...

    Authors: Ksenia Khelik, Karin Lagesen, Geir Kjetil Sandve, Torbjørn Rognes and Alexander Johan Nederbragt

    Citation: BMC Bioinformatics 2017 18:338

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  11. Content type: Methodology Article

    Insecticide resistance is a substantial problem in controlling agricultural and medical pests. Detecting target site mutations is crucial to manage insecticide resistance. Though PCR-based methods have been wi...

    Authors: Dianhao Guo, Jiapeng Luo, Yuenan Zhou, Huamei Xiao, Kang He, Chuanlin Yin, Jianhua Xu and Fei Li

    Citation: BMC Bioinformatics 2017 18:330

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  12. Content type: Methodology Article

    Tn-Seq is a high throughput technique for analysis of transposon mutant libraries to determine conditional essentiality of a gene under an experimental condition. A special feature of the Tn-seq data is that m...

    Authors: Lili Zhao, Mark T. Anderson, Weisheng Wu, Harry L. T. Mobley and Michael A. Bachman

    Citation: BMC Bioinformatics 2017 18:326

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  13. Content type: Software

    Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. The higher the quality of a reference genome assembly the more accurate the downstream...

    Authors: Yuxuan Yuan, Philipp E. Bayer, Armin Scheben, Chon-Kit Kenneth Chan and David Edwards

    Citation: BMC Bioinformatics 2017 18:323

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  14. Content type: Software

    The demand for processing ever increasing amounts of genomic data has raised new challenges for the implementation of highly scalable and efficient computational systems. In this paper we propose SparkBLAST, a...

    Authors: Marcelo Rodrigo de Castro, Catherine dos Santos Tostes, Alberto M. R. Dávila, Hermes Senger and Fabricio A. B. da Silva

    Citation: BMC Bioinformatics 2017 18:318

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  15. Content type: Software

    Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multipl...

    Authors: Kai Battenberg, Ernest K. Lee, Joanna C. Chiu, Alison M. Berry and Daniel Potter

    Citation: BMC Bioinformatics 2017 18:310

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  16. Content type: Software

    The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration...

    Authors: Atul Kamboj, Claus V. Hallwirth, Ian E. Alexander, Geoffrey B. McCowage and Belinda Kramer

    Citation: BMC Bioinformatics 2017 18:305

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  17. Content type: Research Article

    CRISPR is a versatile gene editing tool which has revolutionized genetic research in the past few years. Optimizing sgRNA design to improve the efficiency of target/DNA cleavage is critical to ensure the succe...

    Authors: Pei Fen Kuan, Scott Powers, Shuyao He, Kaiqiao Li, Xiaoyu Zhao and Bo Huang

    Citation: BMC Bioinformatics 2017 18:297

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