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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: Software

    The identification of copy number variants (CNVs) is essential to study human genetic variation and to understand the genetic basis of mendelian disorders and cancers. At present, genome-wide detection of CNVs...

    Authors: Valerio Orlandini, Aldesia Provenzano, Sabrina Giglio and Alberto Magi

    Citation: BMC Bioinformatics 2017 18:321

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  2. Content type: Research article

    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...

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

    Citation: BMC Bioinformatics 2017 18:300

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  3. Content type: Software

    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...

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

    Citation: BMC Bioinformatics 2017 18:296

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  4. Content type: Research Article

    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...

    Authors: Frank Keul, Martin Hess, Michael Goesele and Kay Hamacher

    Citation: BMC Bioinformatics 2017 18:293

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  5. Content type: Research article

    Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have creat...

    Authors: Fatima Zare, Michelle Dow, Nicholas Monteleone, Abdelrahman Hosny and Sheida Nabavi

    Citation: BMC Bioinformatics 2017 18:286

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  6. Content type: Research Article

    Microbiome studies commonly use 16S rRNA gene amplicon sequencing to characterize microbial communities. Errors introduced at multiple steps in this process can affect the interpretation of the data. Here we e...

    Authors: Jonathan L. Golob, Elisa Margolis, Noah G. Hoffman and David N. Fredricks

    Citation: BMC Bioinformatics 2017 18:283

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  7. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:270

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  8. Content type: Research Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:264

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  9. Content type: Research Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:263

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  10. Content type: Commentary

    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...

    Authors: Ian H. Holmes

    Citation: BMC Bioinformatics 2017 18:255

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  11. Content type: Methodology Article

    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, ...

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

    Citation: BMC Bioinformatics 2017 18:258

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  12. Content type: Software

    Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provid...

    Authors: Xiang Gao, Huaiying Lin, Kashi Revanna and Qunfeng Dong

    Citation: BMC Bioinformatics 2017 18:247

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  13. Content type: Research Article

    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...

    Authors: Jing Liu, Yaxiong Chi, Chen Zhu and Yaochu Jin

    Citation: BMC Bioinformatics 2017 18:241

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  14. Content type: Software

    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...

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

    Citation: BMC Bioinformatics 2017 18:242

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  15. Content type: Database

    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...

    Authors: 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

    Citation: BMC Bioinformatics 2017 18:240

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