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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. 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

    Content type: Software

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  2. 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

    Content type: Software

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  3. 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

    Content type: Methodology Article

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  4. 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

    Content type: Software

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  5. 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

    Content type: Software

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  6. 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

    Content type: Software

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  7. 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

    Content type: Software

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  8. 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

    Content type: Research Article

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  9. Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing “outliers” among...

    Authors: Min Wang, Zachary B. Abrams, Steven M. Kornblau and Kevin R. Coombes

    Citation: BMC Bioinformatics 2018 19:9

    Content type: Methodology article

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  10. Genomic imprinting is one of the well-known epigenetic factors causing the association between traits and genes, and has generally been examined by detecting parent-of-origin effects of alleles. A lot of metho...

    Authors: Qi-Lei Zou, Xiao-Ping You, Jian-Long Li, Wing Kam Fung and Ji-Yuan Zhou

    Citation: BMC Bioinformatics 2018 19:8

    Content type: Research Article

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  11. ‘Next-generation’ (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer. The Ion Torrent-based (IONT) platform is among NGS technologies employed in ...

    Authors: Aditya Deshpande, Wenhua Lang, Tina McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F. Anthony San Lucas, Jerry Fowler, Humam Kadara and Paul Scheet

    Citation: BMC Bioinformatics 2018 19:5

    Content type: Methodology Article

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  12. De novo prediction of Transcription Factor Binding Sites (TFBS) using computational methods is a difficult task and it is an important problem in Bioinformatics. The correct recognition of TFBS plays an important...

    Authors: Jader M. Caldonazzo Garbelini, André Y. Kashiwabara and Danilo S. Sanches

    Citation: BMC Bioinformatics 2018 19:4

    Content type: Software

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  13. Genotyping-by-sequencing (GBS), a method to identify genetic variants and quickly genotype samples, reduces genome complexity by using restriction enzymes to divide the genome into fragments whose ends are seq...

    Authors: Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers and Matthew E. Hudson

    Citation: BMC Bioinformatics 2017 18:586

    Content type: Methodology article

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  14. The next generation sequencing (NGS) techniques have been around for over a decade. Many of their fundamental applications rely on the ability to compute good genome assemblies. As the technology evolves, the ...

    Authors: Nilesh Khiste and Lucian Ilie

    Citation: BMC Bioinformatics 2017 18:564

    Content type: Research Article

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  15. The spatial Principal Component Analysis (sPCA, Jombart (Heredity 101:92-103, 2008) is designed to investigate non-random spatial distributions of genetic variation. Unfortunately, the associated tests used fo...

    Authors: V. Montano and T. Jombart

    Citation: BMC Bioinformatics 2017 18:562

    Content type: Methodology Article

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  16. One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, fu...

    Authors: Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol and Gregory Bonito

    Citation: BMC Bioinformatics 2017 18:538

    Content type: Methodology Article

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  17. High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Cur...

    Authors: Janna L. Fierst and Duncan A. Murdock

    Citation: BMC Bioinformatics 2017 18:533

    Content type: Methodology Article

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  18. High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing. Because, errors may r...

    Authors: Yao-Ting Huang and Yu-Wen Huang

    Citation: BMC Bioinformatics 2017 18:524

    Content type: Methodology Article

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  19. Mantle Cell Lymphoma (MCL) is a B cell aggressive neoplasia accounting for about the 6% of all lymphomas. The most common molecular marker of clonality in MCL, as in other B lymphoproliferative disorders, is t...

    Authors: Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo, Daniela Barbero, Mario Boccadoro, Marco Ladetto, Raffaele Calogero, Simone Ferrero and Francesca Cordero

    Citation: BMC Bioinformatics 2017 18:516

    Content type: Research Article

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  20. The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix a...

    Authors: Nathan Sloat, Jui-Wen Liu and Susan J. Schroeder

    Citation: BMC Bioinformatics 2017 18:504

    Content type: Methodology Article

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  21. Gene expression profiling has led to the definition of breast cancer molecular subtypes: Basal-like, HER2-enriched, LuminalA, LuminalB and Normal-like. Different subtypes exhibit diverse responses to treatment...

    Authors: Liying Yang, Yunyan Shen, Xiguo Yuan, Junying Zhang and Jianhua Wei

    Citation: BMC Bioinformatics 2017 18:481

    Content type: Research Article

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  22. De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-mem...

    Authors: Chang Sik Kim, Martyn D. Winn, Vipin Sachdeva and Kirk E. Jordan

    Citation: BMC Bioinformatics 2017 18:467

    Content type: Methodology Article

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  23. Biomedical named entity recognition(BNER) is a crucial initial step of information extraction in biomedical domain. The task is typically modeled as a sequence labeling problem. Various machine learning algori...

    Authors: Chen Lyu, Bo Chen, Yafeng Ren and Donghong Ji

    Citation: BMC Bioinformatics 2017 18:462

    Content type: Research Article

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  24. Detection of important functional and/or structural elements and identification of their positions in a large eukaryotic genomic sequence are an active research area. Gene is an important functional and struct...

    Authors: Biswanath Chowdhury, Arnav Garai and Gautam Garai

    Citation: BMC Bioinformatics 2017 18:460

    Content type: Methodology Article

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  25. Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accum...

    Authors: Yahya Bokhari and Tomasz Arodz

    Citation: BMC Bioinformatics 2017 18:458

    Content type: Methodology Article

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  26. Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perfor...

    Authors: Scott Christley, Mikhail K. Levin, Inimary T. Toby, John M. Fonner, Nancy L. Monson, William H. Rounds, Florian Rubelt, Walter Scarborough, Richard H. Scheuermann and Lindsay G. Cowell

    Citation: BMC Bioinformatics 2017 18:448

    Content type: Software

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  27. Geminiviruses infect a broad range of cultivated and non-cultivated plants, causing significant economic losses worldwide. The studies of the diversity of species, taxonomy, mechanisms of evolution, geographic...

    Authors: José Cleydson F. Silva, Thales F. M. Carvalho, Elizabeth P. B. Fontes and Fabio R. Cerqueira

    Citation: BMC Bioinformatics 2017 18:431

    Content type: Methodology Article

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  28. Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have b...

    Authors: Ying Wang, Kun Wang, Yang Young Lu and Fengzhu Sun

    Citation: BMC Bioinformatics 2017 18:425

    Content type: Methodology Article

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  29. Prediction of DNA-binding residue is important for understanding the protein-DNA recognition mechanism. Many computational methods have been proposed for the prediction, but most of them do not consider the re...

    Authors: Jiyun Zhou, Qin Lu, Ruifeng Xu, Yulan He and Hongpeng Wang

    Citation: BMC Bioinformatics 2017 18:379

    Content type: Research Article

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  30. Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done bef...

    Authors: Saghi Nojoomi and Patrice Koehl

    Citation: BMC Bioinformatics 2017 18:378

    Content type: Methodology Article

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  31. A multivariate genome-wide association test is proposed for analyzing data on multivariate quantitative phenotypes collected from related subjects. The proposed method is a two-step approach. The first step mo...

    Authors: James J. Yang, L Keoki Williams and Anne Buu

    Citation: BMC Bioinformatics 2017 18:376

    Content type: Methodology Article

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  32. Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data. The key idea is that downstream analysis tools such as de novo genome assemblers benefit from a reduced err...

    Authors: Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer and Jan Fostier

    Citation: BMC Bioinformatics 2017 18:374

    Content type: Research Article

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  33. Multi-label classification has recently gained great attention in diverse fields of research, e.g., in biomedical application such as protein function prediction or drug resistance testing in HIV. In this cont...

    Authors: Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch and Dominik Heider

    Citation: BMC Bioinformatics 2017 18:371

    Content type: Software

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  34. Drug resistance in HIV treatment is still a worldwide problem. Predicting resistance to antiretrovirals (ARVs) before starting any treatment is important. Prediction accuracy is essential, as low-accuracy pred...

    Authors: Olivier Sheik Amamuddy, Nigel T. Bishop and Özlem Tastan Bishop

    Citation: BMC Bioinformatics 2017 18:369

    Content type: Research Article

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  35. Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density...

    Authors: Gregory J. Zynda, Jawon Song, Lorenzo Concia, Emily E. Wear, Linda Hanley-Bowdoin, William F. Thompson and Matthew W. Vaughn

    Citation: BMC Bioinformatics 2017 18:362

    Content type: Software

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