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. Methodology Article

    Quasi-linear score for capturing heterogeneous structure in biomarkers

    Linear scores are widely used to predict dichotomous outcomes in biomedical studies because of their learnability and understandability. Such approaches, however, cannot be used to elucidate biodiversity when ...

    Katsuhiro Omae, Osamu Komori and Shinto Eguchi

    BMC Bioinformatics 2017 18:308

    Published on: 19 June 2017

  2. Research article

    Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences

    DNA-binding proteins perform important functions in a great number of biological activities. DNA-binding proteins can interact with ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA), and DNA-binding p...

    Wei Wang, Lin Sun, Shiguang Zhang, Hongjun Zhang, Jinling Shi, Tianhe Xu and Keliang Li

    BMC Bioinformatics 2017 18:300

    Published on: 12 June 2017

  3. Software

    NaviSE: superenhancer navigator integrating epigenomics signal algebra

    Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipeli...

    Alex M. Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta and Marcos J. Araúzo-Bravo

    BMC Bioinformatics 2017 18:296

    Published on: 6 June 2017

  4. Research Article

    PFASUM: a substitution matrix from Pfam structural alignments

    Detecting homologous protein sequences and computing multiple sequence alignments (MSA) are fundamental tasks in molecular bioinformatics. These tasks usually require a substitution matrix for modeling evoluti...

    Frank Keul, Martin Hess, Michael Goesele and Kay Hamacher

    BMC Bioinformatics 2017 18:293

    Published on: 5 June 2017

  5. Methodology Article

    DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

    The development of single-cell RNA sequencing has enabled profound discoveries in biology, ranging from the dissection of the composition of complex tissues to the identification of novel cell types and dynami...

    Zhuo Wang, Shuilin Jin, Guiyou Liu, Xiurui Zhang, Nan Wang, Deliang Wu, Yang Hu, Chiping Zhang, Qinghua Jiang, Li Xu and Yadong Wang

    BMC Bioinformatics 2017 18:270

    Published on: 23 May 2017

  6. Research Article

    Coordinates and intervals in graph-based reference genomes

    It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represe...

    Knut D. Rand, Ivar Grytten, Alexander J. Nederbragt, Geir O. Storvik, Ingrid K. Glad and Geir K. Sandve

    BMC Bioinformatics 2017 18:263

    Published on: 18 May 2017

  7. Research Article

    The rainfall plot: its motivation, characteristics and pitfalls

    A visualization referred to as rainfall plot has recently gained popularity in genome data analysis. The plot is mostly used for illustrating the distribution of somatic cancer mutations along a reference geno...

    Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig and Geir Kjetil Sandve

    BMC Bioinformatics 2017 18:264

    Published on: 18 May 2017

  8. Methodology Article

    HLAscan: genotyping of the HLA region using next-generation sequencing data

    Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, ...

    Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim and Jongsun Jung

    BMC Bioinformatics 2017 18:258

    Published on: 12 May 2017

  9. Commentary

    Solving the master equation for Indels

    Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that a...

    Ian H. Holmes

    BMC Bioinformatics 2017 18:255

    Published on: 12 May 2017

  10. Software

    ImmunoNodes – graphical development of complex immunoinformatics workflows

    Immunoinformatics has become a crucial part in biomedical research. Yet many immunoinformatics tools have command line interfaces only and can be difficult to install. Web-based immunoinformatics tools, on the...

    Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer and Oliver Kohlbacher

    BMC Bioinformatics 2017 18:242

    Published on: 8 May 2017

  11. Research Article

    A time series driven decomposed evolutionary optimization approach for reconstructing large-scale gene regulatory networks based on fuzzy cognitive maps

    Reconstructing gene regulatory networks (GRNs) from expression data plays an important role in understanding the fundamental cellular processes and revealing the underlying relations among genes. Although many...

    Jing Liu, Yaxiong Chi, Chen Zhu and Yaochu Jin

    BMC Bioinformatics 2017 18:241

    Published on: 8 May 2017

  12. Database

    Geminivirus data warehouse: a database enriched with machine learning approaches

    The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible fo...

    Jose Cleydson F. Silva, Thales F. M. Carvalho, Marcos F. Basso, Michihito Deguchi, Welison A. Pereira, Roberto R. Sobrinho, Pedro M. P. Vidigal, Otávio J. B. Brustolini, Fabyano F. Silva, Maximiller Dal-Bianco, Renildes L. F. Fontes, Anésia A. Santos, Francisco Murilo Zerbini, Fabio R. Cerqueira and Elizabeth P. B. Fontes

    BMC Bioinformatics 2017 18:240

    Published on: 5 May 2017

  13. Software

    microTaboo: a general and practical solution to the k-disjoint problem

    A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting....

    Mohammed Al-Jaff, Eric Sandström and Manfred Grabherr

    BMC Bioinformatics 2017 18:228

    Published on: 2 May 2017

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