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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. Targeted sequencing of discrete gene sets is a cost effective strategy to screen subjects for monogenic forms of disease. One method to achieve this pairs microfluidic PCR with next generation sequencing. The ...

    Authors: Christopher E. Gillies, Edgar A. Otto, Virginia Vega-Warner, Catherine C. Robertson, Simone Sanna-Cherchi, Ali Gharavi, Brendan Crawford, Rajendra Bhimma, Cheryl Winkler, Hyun Min Kang and Matthew G. Sampson

    Citation: BMC Bioinformatics 2016 17:233

    Content type: Methodology article

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  2. Next generation sequencing (NGS) produces massive datasets consisting of billions of reads and up to thousands of samples. Subsequent bioinformatic analysis is typically done with the help of open source tools...

    Authors: Masaomi Hatakeyama, Lennart Opitz, Giancarlo Russo, Weihong Qi, Ralph Schlapbach and Hubert Rehrauer

    Citation: BMC Bioinformatics 2016 17:228

    Content type: Software

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  3. Genomic regions with recurrent DNA copy number variations (CNVs) are generally believed to encode oncogenes and tumor suppressor genes (TSGs) that drive cancer growth. However, it remains a challenge to deline...

    Authors: Liangcai Zhang, Ying Yuan, Karen H. Lu and Li Zhang

    Citation: BMC Bioinformatics 2016 17:222

    Content type: Methodology article

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  4. A number of large genomic datasets are being generated for studies of human ancestry and diseases. The ADMIXTURE program is commonly used to infer individual ancestry from genomic data.

    Authors: Suyash S. Shringarpure, Carlos D. Bustamante, Kenneth Lange and David H. Alexander

    Citation: BMC Bioinformatics 2016 17:218

    Content type: Software

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  5. In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNA...

    Authors: Ladislav Rampášek, Randi M. Jimenez, Andrej Lupták, Tomáš Vinař and Broňa Brejová

    Citation: BMC Bioinformatics 2016 17:216

    Content type: Methodology Article

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  6. Detecting and visualizing nonlinear interaction effects of single nucleotide polymorphisms (SNPs) or epistatic interactions are important topics in bioinformatics since they play an important role in unravelin...

    Authors: Junliang Shang, Yingxia Sun, Jin-Xing Liu, Junfeng Xia, Junying Zhang and Chun-Hou Zheng

    Citation: BMC Bioinformatics 2016 17:214

    Content type: Methodology article

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  7. The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S rRNA gene amplicon sequencing). Denoising,...

    Authors: Mohamed Mysara, Natalie Leys, Jeroen Raes and Pieter Monsieurs

    Citation: BMC Bioinformatics 2016 17:192

    Content type: Research article

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  8. Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in alignment of ITD-containing reads to the reference genome. Th...

    Authors: Navin Rustagi, Oliver A Hampton, Jie Li, Liu Xi, Richard A. Gibbs, Sharon E. Plon, Marek Kimmel and David A. Wheeler

    Citation: BMC Bioinformatics 2016 17:188

    Content type: Methodology article

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  9. Amplicon pyrosequencing targets a known genetic region and thus inherently produces reads highly anticipated to have certain features, such as conserved nucleotide sequence, and in the case of protein coding D...

    Authors: Thomas S. Rask, Bent Petersen, Donald S. Chen, Karen P. Day and Anders Gorm Pedersen

    Citation: BMC Bioinformatics 2016 17:176

    Content type: Methodology article

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  10. Compound Heterozygosity (CH) in classical genetics is the presence of two different recessive mutations at a particular gene locus. A relaxed form of CH alleles may account for an essential proportion of the m...

    Authors: Kaiyin Zhong, Lennart C. Karssen, Manfred Kayser and Fan Liu

    Citation: BMC Bioinformatics 2016 17:156

    Content type: Software

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  11. Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and ...

    Authors: Joost B. Beltman, Jos Urbanus, Arno Velds, Nienke van Rooij, Jan C. Rohr, Shalin H. Naik and Ton N. Schumacher

    Citation: BMC Bioinformatics 2016 17:151

    Content type: Methodology article

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  12. Massive parallel sequencing of transcriptomes, revealed the presence of many miRNAs and miRNAs variants named isomiRs with a potential role in several cellular processes through their interaction with a target...

    Authors: Gianvito Urgese, Giulia Paciello, Andrea Acquaviva and Elisa Ficarra

    Citation: BMC Bioinformatics 2016 17:148

    Content type: Software

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  13. High-throughput bio-OMIC technologies are producing high-dimension data from bio-samples at an ever increasing rate, whereas the training sample number in a traditional experiment remains small due to various ...

    Authors: Ruiquan Ge, Manli Zhou, Youxi Luo, Qinghan Meng, Guoqin Mai, Dongli Ma, Guoqing Wang and Fengfeng Zhou

    Citation: BMC Bioinformatics 2016 17:142

    Content type: Methodology article

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  14. Illumina’s sequencing platforms are currently the most utilised sequencing systems worldwide. The technology has rapidly evolved over recent years and provides high throughput at low costs with increasing read...

    Authors: Melanie Schirmer, Rosalinda D’Amore, Umer Z. Ijaz, Neil Hall and Christopher Quince

    Citation: BMC Bioinformatics 2016 17:125

    Content type: Research Article

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  15. We examine several of the choices that went into the design of tDRmapper, a recently reported tool for identifying transfer RNA (tRNA) fragments in deep sequencing data, evaluate them in the context of current...

    Authors: Aristeidis G. Telonis, Phillipe Loher, Yohei Kirino and Isidore Rigoutsos

    Citation: BMC Bioinformatics 2016 17:123

    Content type: Correspondence

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  16. The massive accumulation of protein sequences arising from the rapid development of high-throughput sequencing, coupled with automatic annotation, results in high levels of incorrect annotations. In this study...

    Authors: Ivan Vujaklija, Ana Bielen, Tina Paradžik, Siniša Biđin, Pavle Goldstein and Dušica Vujaklija

    Citation: BMC Bioinformatics 2016 17:91

    Content type: Methodology article

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  17. The second Chargaff’s parity rule and its extensions are recognized as universal phenomena in DNA sequences. However, parity of the frequencies of reverse complementary oligonucleotides could be a mere consequ...

    Authors: Vera Afreixo, João M. O. S. Rodrigues, Carlos A. C. Bastos and Raquel M. Silva

    Citation: BMC Bioinformatics 2016 17:59

    Content type: Research Article

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  18. Traditional Sanger sequencing has been used as a gold standard method for genetic testing in clinic to perform single gene test, which has been a cumbersome and expensive method to test several genes in hetero...

    Authors: Ram Vinay Pandey, Stephan Pabinger, Albert Kriegner and Andreas Weinhäusel

    Citation: BMC Bioinformatics 2016 17:56

    Content type: Software

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  19. Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT...

    Authors: Elo Leung, Amy Huang, Eithon Cadag, Aldrin Montana, Jan Lorenz Soliman and Carol L. Ecale Zhou

    Citation: BMC Bioinformatics 2016 17:43

    Content type: Software

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  20. Next-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of ind...

    Authors: Francisco Pina-Martins, Bruno M. Vieira, Sofia G. Seabra, Dora Batista and Octávio S. Paulo

    Citation: BMC Bioinformatics 2016 17:41

    Content type: Software

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  21. As sequencing technologies can help researchers detect common and rare variants across the human genome in many individuals, it is known that jointly calling genotypes across multiple individuals based on link...

    Authors: Lun-Ching Chang, Bingshan Li, Zhou Fang, Scott Vrieze, Matt McGue, William G. Iacono, George C. Tseng and Wei Chen

    Citation: BMC Bioinformatics 2016 17:37

    Content type: Methodology article

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  22. Transcripts, which have been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with the underlying genomic sequence. These have been identified in a wide variety of tissues...

    Authors: Osagie G. Izuogu, Abd A. Alhasan, Hani M. Alafghani, Mauro Santibanez-Koref, David J. Elliott and Michael S. Jackson

    Citation: BMC Bioinformatics 2016 17:31

    Content type: Software

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    The Erratum to this article has been published in BMC Bioinformatics 2016 17:92

  23. With its simple library preparation and robust approach to genome reduction, genotyping-by-sequencing (GBS) is a flexible and cost-effective strategy for SNP discovery and genotyping, provided an appropriate r...

    Authors: Arthur T. O. Melo, Radhika Bartaula and Iago Hale

    Citation: BMC Bioinformatics 2016 17:29

    Content type: Methodology article

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  24. Transcription factors (TFs) are important regulatory proteins that govern transcriptional regulation. Today, it is known that in higher organisms different TFs have to cooperate rather than acting individually...

    Authors: Cornelia Meckbach, Rebecca Tacke, Xu Hua, Stephan Waack, Edgar Wingender and Mehmet Gültas

    Citation: BMC Bioinformatics 2015 16:400

    Content type: Methodology Article

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  25. Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institu...

    Authors: Dhany Saputra, Simon Rasmussen, Mette V. Larsen, Nizar Haddad, Maria Maddalena Sperotto, Frank M. Aarestrup, Ole Lund and Thomas Sicheritz-Pontén

    Citation: BMC Bioinformatics 2015 16:398

    Content type: Methodology Article

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  26. Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial ...

    Authors: Linda Dib, Xavier Meyer, Panu Artimo, Vassilios Ioannidis, Heinz Stockinger and Nicolas Salamin

    Citation: BMC Bioinformatics 2015 16:394

    Content type: Software

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  27. The alignment of multiple protein sequences is one of the most commonly performed tasks in bioinformatics. In spite of considerable research and efforts that have been recently deployed for improving the perfo...

    Authors: Mufleh Al-Shatnawi, M. Omair Ahmad and M. N. S. Swamy

    Citation: BMC Bioinformatics 2015 16:393

    Content type: Research Article

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  28. Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA’s 3D structure. Currently the design of RNA molecules, which fold into a specific structure ...

    Authors: Robert Kleinkauf, Torsten Houwaart, Rolf Backofen and Martin Mann

    Citation: BMC Bioinformatics 2015 16:389

    Content type: Software

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  29. Because of the short read length of high throughput sequencing data, assembly errors are introduced in genome assembly, which may have adverse impact to the downstream data analysis. Several tools have been de...

    Authors: Xiao Zhu, Henry C. M. Leung, Rongjie Wang, Francis Y. L. Chin, Siu Ming Yiu, Guangri Quan, Yajie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou and Yadong Wang

    Citation: BMC Bioinformatics 2015 16:386

    Content type: Research article

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  30. Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of la...

    Authors: Antonio Ribeiro, Agnieszka Golicz, Christine Anne Hackett, Iain Milne, Gordon Stephen, David Marshall, Andrew J. Flavell and Micha Bayer

    Citation: BMC Bioinformatics 2015 16:382

    Content type: Research Article

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  31. The field of metagenomics (study of genetic material recovered directly from an environment) has grown rapidly, with many bioinformatics analysis methods being developed. To ensure appropriate use of such meth...

    Authors: Michael A. Peabody, Thea Van Rossum, Raymond Lo and Fiona S. L. Brinkman

    Citation: BMC Bioinformatics 2015 16:362

    Content type: Research

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  32. Over the last decade, next generation sequencing (NGS) has become widely available, and is now the sequencing technology of choice for most researchers. Nonetheless, NGS presents a challenge for the evolutiona...

    Authors: Steven H. Wu and Allen G. Rodrigo

    Citation: BMC Bioinformatics 2015 16:357

    Content type: Methodology article

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  33. Small RNA-sequencing has revealed the diversity and high abundance of small RNAs derived from tRNAs, referred to as tRNA-derived RNAs. However, at present, there is no standardized nomenclature and there are n...

    Authors: Sara R. Selitsky and Praveen Sethupathy

    Citation: BMC Bioinformatics 2015 16:354

    Content type: Methodology article

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