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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: Research article

    The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog...

    Authors: Deborah Galpert, Alberto Fernández, Francisco Herrera, Agostinho Antunes, Reinaldo Molina-Ruiz and Guillermin Agüero-Chapin

    Citation: BMC Bioinformatics 2018 19:166

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  2. Content type: Methodology article

    Activation induced deaminase (AID) and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) are deaminases that mutate C to U on single-stranded DNA (ssDNA). AID is expressed primarily ...

    Authors: Maxwell Shapiro, Stephen Meier and Thomas MacCarthy

    Citation: BMC Bioinformatics 2018 19:163

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    The Correction to this article has been published in BMC Bioinformatics 2018 19:256

  3. Content type: Software

    Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together wit...

    Authors: Jan Budczies, Nicole Pfarr, Eva Romanovsky, Volker Endris, Albrecht Stenzinger and Carsten Denkert

    Citation: BMC Bioinformatics 2018 19:157

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  4. Content type: Research article

    Detailed modelling of the neutral mutational process in cancer cells is crucial for identifying driver mutations and understanding the mutational mechanisms that act during cancer development. The neutral muta...

    Authors: Johanna Bertl, Qianyun Guo, Malene Juul, Søren Besenbacher, Morten Muhlig Nielsen, Henrik Hornshøj, Jakob Skou Pedersen and Asger Hobolth

    Citation: BMC Bioinformatics 2018 19:147

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  5. Content type: Methodology

    Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments where adjacent segments have different properties, such as different mean value...

    Authors: Senthil B. Girimurugan, Yuhang Liu, Pei-Yau Lung, Daniel L. Vera, Jonathan H. Dennis, Hank W. Bass and Jinfeng Zhang

    Citation: BMC Bioinformatics 2018 19:131

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  6. Content type: Methodology article

    Intraspecific variation in ploidy occurs in a wide range of species including pathogenic and nonpathogenic eukaryotes such as yeasts and oomycetes. Ploidy can be inferred indirectly - without measuring DNA con...

    Authors: Clemens L. Weiß, Marina Pais, Liliana M. Cano, Sophien Kamoun and Hernán A. Burbano

    Citation: BMC Bioinformatics 2018 19:122

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  7. Content type: Software

    DNA methylation is an important epigenetic modification critical in regulation and transgenerational inheritance. The methylation level can be estimated at single-nucleotide resolution by whole-genome bisulfit...

    Authors: Kevin Yu Yuan Huang, Yan-Jiun Huang and Pao-Yang Chen

    Citation: BMC Bioinformatics 2018 19:111

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  8. Content type: Research article

    DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however hav...

    Authors: Ingo Bulla, Benoît Aliaga, Virginia Lacal, Jan Bulla, Christoph Grunau and Cristian Chaparro

    Citation: BMC Bioinformatics 2018 19:105

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  9. Content type: Software

    Prioritization of sequence variants for diagnosis and discovery of Mendelian diseases is challenging, especially in large collections of whole genome sequences (WGS). Fast, scalable solutions are needed for di...

    Authors: Steven Flygare, Edgar Javier Hernandez, Lon Phan, Barry Moore, Man Li, Anthony Fejes, Hao Hu, Karen Eilbeck, Chad Huff, Lynn Jorde, Martin G. Reese and Mark Yandell

    Citation: BMC Bioinformatics 2018 19:57

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  10. Content type: Software

    The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally a...

    Authors: Raúl Arias-Carrasco, Yessenia Vásquez-Morán, Helder I. Nakaya and Vinicius Maracaja-Coutinho

    Citation: BMC Bioinformatics 2018 19:55

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  11. Content type: Methodology Article

    Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the con...

    Authors: Jeremy R. Wang, James Holt, Leonard McMillan and Corbin D. Jones

    Citation: BMC Bioinformatics 2018 19:50

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  12. Content type: Software

    Over the last few decades, computational genomics has tremendously contributed to decipher biology from genome sequences and related data. Considerable effort has been devoted to the prediction of transcriptio...

    Authors: Marco Di Salvo, Eva Pinatel, Adelfia Talà, Marco Fondi, Clelia Peano and Pietro Alifano

    Citation: BMC Bioinformatics 2018 19:36

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  13. Content type: Software

    Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use ...

    Authors: David E. Condon, Phu V. Tran, Yu-Chin Lien, Jonathan Schug, Michael K. Georgieff, Rebecca A. Simmons and Kyoung-Jae Won

    Citation: BMC Bioinformatics 2018 19:31

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  14. Content type: Software

    Genomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based ...

    Authors: Eliot C. Bush, Anne E. Clark, Carissa A. DeRanek, Alexander Eng, Juliet Forman, Kevin Heath, Alexander B. Lee, Daniel M. Stoebel, Zunyan Wang, Matthew Wilber and Helen Wu

    Citation: BMC Bioinformatics 2018 19:32

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  15. Content type: Software

    GenIO is a novel web-server, designed to assist clinical genomics researchers and medical doctors in the diagnostic process of rare genetic diseases. The tool identifies the most probable variants causing a ra...

    Authors: Daniel Koile, Marta Cordoba, Maximiliano de Sousa Serro, Marcelo Andres Kauffman and Patricio Yankilevich

    Citation: BMC Bioinformatics 2018 19:25

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  16. Content type: Research Article

    The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity...

    Authors: Guido Zampieri, Dinh Van Tran, Michele Donini, Nicolò Navarin, Fabio Aiolli, Alessandro Sperduti and Giorgio Valle

    Citation: BMC Bioinformatics 2018 19:23

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Page 2 of 22

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)

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    1405 Usage Factor


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