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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

    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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. Content type: Research Article

    Nowadays, many public repositories containing large microarray gene expression datasets are available. However, the problem lies in the fact that microarray technology are less powerful and accurate than more ...

    Authors: Daniel Castillo, Juan Manuel Gálvez, Luis Javier Herrera, Belén San Román, Fernando Rojas and Ignacio Rojas

    Citation: BMC Bioinformatics 2017 18:506

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  10. 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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  11. Content type: Software

    The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexe...

    Authors: Tao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo and Rui Zhang

    Citation: BMC Bioinformatics 2017 18:482

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  12. Content type: Software

    Large scale bacterial sequencing has made the determination of genetic relationships within large sequence collections of bacterial genomes derived from the same microbial species an increasingly common task. ...

    Authors: Oriol Mazariegos-Canellas, Trien Do, Tim Peto, David W. Eyre, Anthony Underwood, Derrick Crook and David H. Wyllie

    Citation: BMC Bioinformatics 2017 18:477

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  13. Content type: Database

    Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009...

    Authors: Oana Carja, Tongji Xing, Edward W. J. Wallace, Joshua B. Plotkin and Premal Shah

    Citation: BMC Bioinformatics 2017 18:461

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  14. Content type: Research Article

    Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene ...

    Authors: Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou and Kui Lin

    Citation: BMC Bioinformatics 2017 18:439

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  15. Content type: Software

    Copy number variations (CNVs) are the main genetic structural variations in cancer genome. Detecting CNVs in genetic exome region is efficient and cost-effective in identifying cancer associated genes. Many to...

    Authors: Jianing Gao, Changlin Wan, Huan Zhang, Ao Li, Qiguang Zang, Rongjun Ban, Asim Ali, Zhenghua Yu, Qinghua Shi, Xiaohua Jiang and Yuanwei Zhang

    Citation: BMC Bioinformatics 2017 18:436

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  16. Content type: Software

    Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the inter...

    Authors: Alan Beccati, Jan Gerken, Christian Quast, Pelin Yilmaz and Frank Oliver Glöckner

    Citation: BMC Bioinformatics 2017 18:433

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