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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

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

    Gene expression profiling has led to the definition of breast cancer molecular subtypes: Basal-like, HER2-enriched, LuminalA, LuminalB and Normal-like. Different subtypes exhibit diverse responses to treatment...

    Authors: Liying Yang, Yunyan Shen, Xiguo Yuan, Junying Zhang and Jianhua Wei

    Citation: BMC Bioinformatics 2017 18:481

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  8. Content type: Methodology Article

    De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-mem...

    Authors: Chang Sik Kim, Martyn D. Winn, Vipin Sachdeva and Kirk E. Jordan

    Citation: BMC Bioinformatics 2017 18:467

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  9. Content type: Research Article

    Biomedical named entity recognition(BNER) is a crucial initial step of information extraction in biomedical domain. The task is typically modeled as a sequence labeling problem. Various machine learning algori...

    Authors: Chen Lyu, Bo Chen, Yafeng Ren and Donghong Ji

    Citation: BMC Bioinformatics 2017 18:462

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  10. Content type: Methodology Article

    Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accum...

    Authors: Yahya Bokhari and Tomasz Arodz

    Citation: BMC Bioinformatics 2017 18:458

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  11. Content type: Methodology Article

    Detection of important functional and/or structural elements and identification of their positions in a large eukaryotic genomic sequence are an active research area. Gene is an important functional and struct...

    Authors: Biswanath Chowdhury, Arnav Garai and Gautam Garai

    Citation: BMC Bioinformatics 2017 18:460

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  12. Content type: Software

    Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perfor...

    Authors: Scott Christley, Mikhail K. Levin, Inimary T. Toby, John M. Fonner, Nancy L. Monson, William H. Rounds, Florian Rubelt, Walter Scarborough, Richard H. Scheuermann and Lindsay G. Cowell

    Citation: BMC Bioinformatics 2017 18:448

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2016 Journal Metrics

  • Citation Impact
    2.448 - 2-year Impact Factor
    3.450 - 5-year Impact Factor
    0.946 - Source Normalized Impact per Paper (SNIP)
    1.467 - SCImago Journal Rank (SJR)

    Usage 
    3784657 downloads
    1405 Usage Factor


    Social Media Impact
    816 mentions

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