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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. Content type: Methodology article

    Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing “outliers” among...

    Authors: Min Wang, Zachary B. Abrams, Steven M. Kornblau and Kevin R. Coombes

    Citation: BMC Bioinformatics 2018 19:9

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  2. Content type: Research Article

    Genomic imprinting is one of the well-known epigenetic factors causing the association between traits and genes, and has generally been examined by detecting parent-of-origin effects of alleles. A lot of metho...

    Authors: Qi-Lei Zou, Xiao-Ping You, Jian-Long Li, Wing Kam Fung and Ji-Yuan Zhou

    Citation: BMC Bioinformatics 2018 19:8

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  3. Content type: Methodology Article

    ‘Next-generation’ (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer. The Ion Torrent-based (IONT) platform is among NGS technologies employed in ...

    Authors: Aditya Deshpande, Wenhua Lang, Tina McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F. Anthony San Lucas, Jerry Fowler, Humam Kadara and Paul Scheet

    Citation: BMC Bioinformatics 2018 19:5

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  4. Content type: Software

    De novo prediction of Transcription Factor Binding Sites (TFBS) using computational methods is a difficult task and it is an important problem in Bioinformatics. The correct recognition of TFBS plays an important...

    Authors: Jader M. Caldonazzo Garbelini, André Y. Kashiwabara and Danilo S. Sanches

    Citation: BMC Bioinformatics 2018 19:4

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  5. Content type: Methodology article

    Genotyping-by-sequencing (GBS), a method to identify genetic variants and quickly genotype samples, reduces genome complexity by using restriction enzymes to divide the genome into fragments whose ends are seq...

    Authors: Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers and Matthew E. Hudson

    Citation: BMC Bioinformatics 2017 18:586

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  6. Content type: Research Article

    The next generation sequencing (NGS) techniques have been around for over a decade. Many of their fundamental applications rely on the ability to compute good genome assemblies. As the technology evolves, the ...

    Authors: Nilesh Khiste and Lucian Ilie

    Citation: BMC Bioinformatics 2017 18:564

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  7. Content type: Methodology Article

    The spatial Principal Component Analysis (sPCA, Jombart (Heredity 101:92-103, 2008) is designed to investigate non-random spatial distributions of genetic variation. Unfortunately, the associated tests used fo...

    Authors: V. Montano and T. Jombart

    Citation: BMC Bioinformatics 2017 18:562

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  8. Content type: Methodology Article

    One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, fu...

    Authors: Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol and Gregory Bonito

    Citation: BMC Bioinformatics 2017 18:538

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  9. Content type: Methodology Article

    High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Cur...

    Authors: Janna L. Fierst and Duncan A. Murdock

    Citation: BMC Bioinformatics 2017 18:533

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  10. Content type: Methodology Article

    High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing. Because, errors may r...

    Authors: Yao-Ting Huang and Yu-Wen Huang

    Citation: BMC Bioinformatics 2017 18:524

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  11. Content type: Research Article

    Mantle Cell Lymphoma (MCL) is a B cell aggressive neoplasia accounting for about the 6% of all lymphomas. The most common molecular marker of clonality in MCL, as in other B lymphoproliferative disorders, is t...

    Authors: Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo, Daniela Barbero, Mario Boccadoro, Marco Ladetto, Raffaele Calogero, Simone Ferrero and Francesca Cordero

    Citation: BMC Bioinformatics 2017 18:516

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  12. Content type: Methodology Article

    The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix a...

    Authors: Nathan Sloat, Jui-Wen Liu and Susan J. Schroeder

    Citation: BMC Bioinformatics 2017 18:504

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