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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: Methodology Article

    Genome-wide association studies (GWASs) have been widely used to discover the genetic basis of complex phenotypes. However, standard single-SNP GWASs suffer from lack of power. In particular, they do not direc...

    Authors: Christine Sinoquet

    Citation: BMC Bioinformatics 2018 19:106

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  2. Content type: Software

    Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by model...

    Authors: Andrey Ziyatdinov, Miquel Vázquez-Santiago, Helena Brunel, Angel Martinez-Perez, Hugues Aschard and Jose Manuel Soria

    Citation: BMC Bioinformatics 2018 19:68

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  3. Content type: Software

    Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep se...

    Authors: Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni and Stefan Bonn

    Citation: BMC Bioinformatics 2018 19:54

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  4. Content type: Research Article

    The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of databases containing sequence data for hundreds of thousands influenza strai...

    Authors: Christopher S. Anderson, Patrick R. McCall, Harry A. Stern, Hongmei Yang and David J. Topham

    Citation: BMC Bioinformatics 2018 19:51

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  5. Content type: Software

    The advent of modern high-throughput genetics continually broadens the gap between the rising volume of sequencing data, and the tools required to process them. The need to pinpoint a small subset of functiona...

    Authors: Monika Mozere, Mehmet Tekman, Jameela Kari, Detlef Bockenhauer, Robert Kleta and Horia Stanescu

    Citation: BMC Bioinformatics 2018 19:46

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  6. Content type: Research Article

    The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly acces...

    Authors: Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart and Paul C. Boutros

    Citation: BMC Bioinformatics 2018 19:28

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  7. Content type: Methodology Article

    Protein or nucleic acid sequences contain a multitude of associated annotations representing continuous sequence elements (CSEs). Comparing these CSEs is needed, whenever we want to match identical annotations...

    Authors: Roman Prytuliak, Friedhelm Pfeiffer and Bianca Hermine Habermann

    Citation: BMC Bioinformatics 2018 19:24

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  8. Content type: Software

    Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results ...

    Authors: Jordi Martorell-Marugan, Daniel Toro-Dominguez, Marta E. Alarcon-Riquelme and Pedro Carmona-Saez

    Citation: BMC Bioinformatics 2017 18:563

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  9. Content type: Software

    High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number ...

    Authors: Kenneth D. Doig, Jason Ellul, Andrew Fellowes, Ella R. Thompson, Georgina Ryland, Piers Blombery, Anthony T. Papenfuss and Stephen B. Fox

    Citation: BMC Bioinformatics 2017 18:555

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  10. Content type: Software

    Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in...

    Authors: Matthias Beyens, Nele Boeckx, Guy Van Camp, Ken Op de Beeck and Geert Vandeweyer

    Citation: BMC Bioinformatics 2017 18:554

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  11. Content type: Software

    Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic...

    Authors: Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang and David Vocadlo

    Citation: BMC Bioinformatics 2017 18:521

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  12. Content type: Software

    Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene thera...

    Authors: Giulio Spinozzi, Andrea Calabria, Stefano Brasca, Stefano Beretta, Ivan Merelli, Luciano Milanesi and Eugenio Montini

    Citation: BMC Bioinformatics 2017 18:520

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  13. Content type: Methodology Article

    Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent ...

    Authors: Megan J. Bowman, Jane A. Pulman, Tiffany L. Liu and Kevin L. Childs

    Citation: BMC Bioinformatics 2017 18:522

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  14. Content type: Software

    With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F1 population. However, based on such genetic maps, quantitative ...

    Authors: Fenxiang Liu, Chunfa Tong, Shentong Tao, Jiyan Wu, Yuhua Chen, Dan Yao, Huogen Li and Jisen Shi

    Citation: BMC Bioinformatics 2017 18:515

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  15. Content type: Methodology Article

    Gene set enrichment analysis and overrepresentation analyses are commonly used methods to determine the biological processes affected by a differential expression experiment. This approach requires biologicall...

    Authors: Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan and Casey S. Greene

    Citation: BMC Bioinformatics 2017 18:512

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  16. Content type: Software

    Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, whil...

    Authors: Kosai Al-Nakeeb, Thomas Nordahl Petersen and Thomas Sicheritz-Pontén

    Citation: BMC Bioinformatics 2017 18:510

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