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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

    Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation and nucleotide mutation due to their repetitive and ...

    Authors: Devika Ganesamoorthy, Minh Duc Cao, Tania Duarte, Wenhan Chen and Lachlan Coin

    Citation: BMC Bioinformatics 2018 19:267

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  2. Content type: Methodology article

    Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombinat...

    Authors: Haojing Shao, Devika Ganesamoorthy, Tania Duarte, Minh Duc Cao, Clive J. Hoggart and Lachlan J. M. Coin

    Citation: BMC Bioinformatics 2018 19:261

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  3. Content type: Methodology article

    Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each ...

    Authors: Panu Somervuo, Patrik Koskinen, Peng Mei, Liisa Holm, Petri Auvinen and Lars Paulin

    Citation: BMC Bioinformatics 2018 19:257

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  4. Content type: Methodology article

    Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays...

    Authors: Stefano Beretta, Murray D. Patterson, Simone Zaccaria, Gianluca Della Vedova and Paola Bonizzoni

    Citation: BMC Bioinformatics 2018 19:252

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  5. Content type: Software

    The advent of next-generation sequencing (NGS) has made whole-genome sequencing of cohorts of individuals a reality. Primary datasets of raw or aligned reads of this sort can get very large. For scientific que...

    Authors: Kristiina Ausmees, Aji John, Salman Z. Toor, Andreas Hellander and Carl Nettelblad

    Citation: BMC Bioinformatics 2018 19:240

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  6. Content type: Research article

    The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transpl...

    Authors: Maria Luisa Matey-Hernandez, Søren Brunak and Jose M. G. Izarzugaza

    Citation: BMC Bioinformatics 2018 19:239

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  7. Content type: Methodology article

    Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of g...

    Authors: Marcel Smid, Robert R. J. Coebergh van den Braak, Harmen J. G. van de Werken, Job van Riet, Anne van Galen, Vanja de Weerd, Michelle van der Vlugt-Daane, Sandra I. Bril, Zarina S. Lalmahomed, Wigard P. Kloosterman, Saskia M. Wilting, John A. Foekens, Jan N. M. IJzermans, John W. M. Martens and Anieta M. Sieuwerts

    Citation: BMC Bioinformatics 2018 19:236

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  8. Content type: Methodology article

    Spastic cerebral palsy (CP) is a leading cause of physical disability. Most people with spastic CP are born with it, but early diagnosis is challenging, and no current biomarker platform readily identifies aff...

    Authors: Erin L. Crowgey, Adam G. Marsh, Karyn G. Robinson, Stephanie K. Yeager and Robert E. Akins

    Citation: BMC Bioinformatics 2018 19:225

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  9. Content type: Research article

    Given a set of t n-length DNA sequences, q satisfying 0 < q ≤ 1, and l and d satisfying 0 ≤ d < l < n, the quorum planted motif search (qPMS) finds l-length strings that occur in at least qt input sequences with ...

    Authors: Qiang Yu, Dingbang Wei and Hongwei Huo

    Citation: BMC Bioinformatics 2018 19:228

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  10. Content type: Methodology article

    With the reduction of gene sequencing cost and demand for emerging technologies such as precision medical treatment and deep learning in genome, it is an era of gene data outbreaks today. How to store, transmi...

    Authors: Qiuming Luo, Chao Guo, Yi Jun Zhang, Ye Cai and Gang Liu

    Citation: BMC Bioinformatics 2018 19:230

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  11. Content type: Research article

    Third generation sequencing technologies generate long reads that exhibit high error rates, in particular for insertions and deletions which are usually the most difficult errors to cope with. The only exact a...

    Authors: Jean-François Gibrat

    Citation: BMC Bioinformatics 2018 19:226

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  12. Content type: Software

    Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by t...

    Authors: Tara N. Furstenau, Jill H. Cocking, Jason W. Sahl and Viacheslav Y. Fofanov

    Citation: BMC Bioinformatics 2018 19:222

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  13. Content type: Methodology article

    Genome annotation is of key importance in many research questions. The identification of protein-coding genes is often based on transcriptome sequencing data, ab-initio or homology-based prediction. Recently, it ...

    Authors: Jens Keilwagen, Frank Hartung, Michael Paulini, Sven O. Twardziok and Jan Grau

    Citation: BMC Bioinformatics 2018 19:189

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Page 1 of 22

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