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Sequence analysis (applications)

Section edited by João Setubal

This section incorporates all aspects of sequence analysis applications, including but not limited to: software, workflows and webservers dealing with applied sequence/genome analysis, sequence assembly, analysis of sequence features, and protein function and ligand binding, estimated through sequence features.

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  1. Reference genome assemblies are valuable, as they provide insights into gene content, genetic evolution and domestication. The higher the quality of a reference genome assembly the more accurate the downstream...

    Authors: Yuxuan Yuan, Philipp E. Bayer, Armin Scheben, Chon-Kit Kenneth Chan and David Edwards

    Citation: BMC Bioinformatics 2017 18:323

    Content type: Software

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  2. The demand for processing ever increasing amounts of genomic data has raised new challenges for the implementation of highly scalable and efficient computational systems. In this paper we propose SparkBLAST, a...

    Authors: Marcelo Rodrigo de Castro, Catherine dos Santos Tostes, Alberto M. R. Dávila, Hermes Senger and Fabricio A. B. da Silva

    Citation: BMC Bioinformatics 2017 18:318

    Content type: Software

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  3. Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multipl...

    Authors: Kai Battenberg, Ernest K. Lee, Joanna C. Chiu, Alison M. Berry and Daniel Potter

    Citation: BMC Bioinformatics 2017 18:310

    Content type: Software

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  4. The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration...

    Authors: Atul Kamboj, Claus V. Hallwirth, Ian E. Alexander, Geoffrey B. McCowage and Belinda Kramer

    Citation: BMC Bioinformatics 2017 18:305

    Content type: Software

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  5. CRISPR is a versatile gene editing tool which has revolutionized genetic research in the past few years. Optimizing sgRNA design to improve the efficiency of target/DNA cleavage is critical to ensure the succe...

    Authors: Pei Fen Kuan, Scott Powers, Shuyao He, Kaiqiao Li, Xiaoyu Zhao and Bo Huang

    Citation: BMC Bioinformatics 2017 18:297

    Content type: Research Article

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  6. Dictyostelium discoideum, a soil-dwelling social amoeba, is a model for the study of numerous biological processes. Research in the field has benefited mightily from the adoption of ne...

    Authors: Miha Stajdohar, Rafael D. Rosengarten, Janez Kokosar, Luka Jeran, Domen Blenkus, Gad Shaulsky and Blaz Zupan

    Citation: BMC Bioinformatics 2017 18:291

    Content type: Software

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  7. Recent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called “microbial dark matter” (microbes that until now have ...

    Authors: Bertjan Broeksema, Magdalena Calusinska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse and Mohammad Ghoniem

    Citation: BMC Bioinformatics 2017 18:233

    Content type: Software

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  8. Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to f...

    Authors: Loris Bertoldi, Claudio Forcato, Nicola Vitulo, Giovanni Birolo, Fabio De Pascale, Erika Feltrin, Riccardo Schiavon, Franca Anglani, Susanna Negrisolo, Alessandra Zanetti, Francesca D’Avanzo, Rosella Tomanin, Georgine Faulkner, Alessandro Vezzi and Giorgio Valle

    Citation: BMC Bioinformatics 2017 18:225

    Content type: Software

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  9. Myc is an essential gene having multiple functions such as in cell growth, differentiation, apoptosis, genomic stability, angiogenesis, and disease biology. A large number of researchers dedicated to Myc biolo...

    Authors: Debangana Chakravorty, Tanmoy Jana, Sukhen Das Mandal, Anuradha Seth, Anubrata Bhattacharya and Sudipto Saha

    Citation: BMC Bioinformatics 2017 18:224

    Content type: Database

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  10. Somatic alterations, including loss of heterozygosity, can affect the expression of oncogenes and tumor suppressor genes. Whole genome sequencing enables detailed characterization of such aberrations. However,...

    Authors: Ebrahim Afyounian, Matti Annala and Matti Nykter

    Citation: BMC Bioinformatics 2017 18:215

    Content type: Software

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  11. Carbohydrate-active enzymes are found in all organisms and participate in key biological processes. These enzymes are classified in 274 families in the CAZy database but the sequence diversity within each fami...

    Authors: P. K. Busk, B. Pilgaard, M. J. Lezyk, A. S. Meyer and L. Lange

    Citation: BMC Bioinformatics 2017 18:214

    Content type: Software

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  12. Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, a...

    Authors: William W. Greenwald, He Li, Erin N. Smith, Paola Benaglio, Naoki Nariai and Kelly A. Frazer

    Citation: BMC Bioinformatics 2017 18:207

    Content type: Software

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  13. A comprehensive map of the human-M. tuberculosis (MTB) protein interactome would help fill the gaps in our understanding of the disease, and computational prediction can aid and complement experimental studies to...

    Authors: Gaurang Mahajan and Shekhar C. Mande

    Citation: BMC Bioinformatics 2017 18:201

    Content type: Research article

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  14. Insecticide resistance is a major challenge for the control program of insect pests in the fields of crop protection, human and animal health etc. Resistance to different insecticides is conferred by the prote...

    Authors: Prabina Kumar Meher, Tanmaya Kumar Sahu, Anjali Banchariya and Atmakuri Ramakrishna Rao

    Citation: BMC Bioinformatics 2017 18:190

    Content type: Research article

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  15. Bacterial sRNA-mediated regulatory networks has been introduced as a powerful way to analyze the fast rewiring capabilities of a bacteria in response to changing environmental conditions. The identification of...

    Authors: Romain Bourqui, Isabelle Dutour, Jonathan Dubois, William Benchimol and Patricia Thébault

    Citation: BMC Bioinformatics 2017 18:188

    Content type: Software

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  16. The rapid progress of high-throughput DNA sequencing techniques has dramatically reduced the costs of whole genome sequencing, which leads to revolutionary advances in gene industry. The explosively increasing...

    Authors: Zhi-An Huang, Zhenkun Wen, Qingjin Deng, Ying Chu, Yiwen Sun and Zexuan Zhu

    Citation: BMC Bioinformatics 2017 18:179

    Content type: Software

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  17. Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several...

    Authors: Emily Jane McTavish, James Pettengill, Steven Davis, Hugh Rand, Errol Strain, Marc Allard and Ruth E. Timme

    Citation: BMC Bioinformatics 2017 18:178

    Content type: Software

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  18. Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and d...

    Authors: Anke Fähnrich, Moritz Krebbel, Normann Decker, Martin Leucker, Felix D. Lange, Kathrin Kalies and Steffen Möller

    Citation: BMC Bioinformatics 2017 18:164

    Content type: Software

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  19. DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of t...

    Authors: Ricardo Olanda, Mariano Pérez, Juan M. Orduña, Joaquín Tárraga and Joaquín Dopazo

    Citation: BMC Bioinformatics 2017 18:161

    Content type: Software

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  20. Several methods have been developed to predict the pathogenicity of missense mutations but none has been specifically designed for classification of variants in mtDNA-encoded polypeptides. Moreover, there is n...

    Authors: Antonio Martín-Navarro, Andrés Gaudioso-Simón, Jorge Álvarez-Jarreta, Julio Montoya, Elvira Mayordomo and Eduardo Ruiz-Pesini

    Citation: BMC Bioinformatics 2017 18:158

    Content type: Research article

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  21. Deriving valid variant calling results from raw next-generation sequencing data is a particularly challenging task, especially with respect to clinical diagnostics and personalized medicine. However, when usin...

    Authors: Sarah Sandmann, Aniek O. de Graaf and Martin Dugas

    Citation: BMC Bioinformatics 2017 18:133

    Content type: Software

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  22. RNA-Seq technology has received a lot of attention in recent years for microalgal global transcriptomic profiling. It is widely used in transcriptome-wide analysis of gene expression., particularly for microal...

    Authors: Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan and Yuan Kun Lee

    Citation: BMC Bioinformatics 2017 18:122

    Content type: Research article

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  23. In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a use...

    Authors: Sergio Gonzalez, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo and Norma Paniego

    Citation: BMC Bioinformatics 2017 18:121

    Content type: Software

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  24. Genome-wide association studies have enabled identification of thousands of loci for hundreds of traits. Yet, for most human traits a substantial part of the estimated heritability is unexplained. This and rec...

    Authors: Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P. Morris and Inga Prokopenko

    Citation: BMC Bioinformatics 2017 18:110

    Content type: Software

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  25. With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides ...

    Authors: Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan and Amjad Ali

    Citation: BMC Bioinformatics 2017 18:106

    Content type: Software

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  26. Next Generation Genome sequencing techniques became affordable for massive sequencing efforts devoted to clinical characterization of human diseases. However, the cost of providing cloud-based data analysis of...

    Authors: Hatem Elshazly, Yassine Souilmi, Peter J. Tonellato, Dennis P. Wall and Mohamed Abouelhoda

    Citation: BMC Bioinformatics 2017 18:49

    Content type: Software

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  27. Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequenc...

    Authors: Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos and Grigoris D. Amoutzias

    Citation: BMC Bioinformatics 2017 18:13

    Content type: Software

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  28. Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this cont...

    Authors: Robin Kobus, Christian Hundt, André Müller and Bertil Schmidt

    Citation: BMC Bioinformatics 2017 18:11

    Content type: Software

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  29. RNA editing is a co-transcriptional modification that increases the molecular diversity, alters secondary structure and protein coding sequences by changing the sequence of transcripts. The most common RNA edi...

    Authors: Michael Piechotta, Emanuel Wyler, Uwe Ohler, Markus Landthaler and Christoph Dieterich

    Citation: BMC Bioinformatics 2017 18:7

    Content type: Software

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  30. The post-genomic era with its wealth of sequences gave rise to a broad range of protein residue-residue contact detecting methods. Although various coevolution methods such as PSICOV, DCA and plmDCA provide co...

    Authors: Reda Rawi, Raghvendra Mall, Khalid Kunji, Mohammed El Anbari, Michael Aupetit, Ehsan Ullah and Halima Bensmail

    Citation: BMC Bioinformatics 2016 17:533

    Content type: Research Article

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  31. Power calculators are currently available for the design of genetic association studies of binary phenotypes and quantitative traits, but not for “time to event” outcomes, which are of particular relevance in ...

    Authors: Hamzah Syed, Andrea L. Jorgensen and Andrew P. Morris

    Citation: BMC Bioinformatics 2016 17:523

    Content type: Software

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  32. Transcription factors (TFs) form complexes that bind regulatory modules (RMs) within DNA, to control specific sets of genes. Some transcription factor binding sites (TFBSs) near the transcription start site (T...

    Authors: Natalia Acevedo-Luna, Leonardo Mariño-Ramírez, Armand Halbert, Ulla Hansen, David Landsman and John L. Spouge

    Citation: BMC Bioinformatics 2016 17:479

    Content type: Research article

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  33. Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipe...

    Authors: Jiwoong Kim, Min Soo Kim, Andrew Y. Koh, Yang Xie and Xiaowei Zhan

    Citation: BMC Bioinformatics 2016 17:420

    Content type: Software

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  34. The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily enc...

    Authors: Charles Girardot, Jelle Scholtalbers, Sajoscha Sauer, Shu-Yi Su and Eileen E.M. Furlong

    Citation: BMC Bioinformatics 2016 17:419

    Content type: Software

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  35. RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs w...

    Authors: Pritha Ghosh, Oommen K. Mathew and Ramanathan Sowdhamini

    Citation: BMC Bioinformatics 2016 17:411

    Content type: Software

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  36. Transcription factor binding, histone modification, and chromatin accessibility studies are important approaches to understanding the biology of gene regulation. ChIP-seq and DNase-seq have become the standard...

    Authors: Qian Qin, Shenglin Mei, Qiu Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu, Chongzhi Zang, Han Xu, Yiwen Chen, Clifford A. Meyer, Yong Zhang, Myles Brown, Henry W. Long…

    Citation: BMC Bioinformatics 2016 17:404

    Content type: Software

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  37. The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical comp...

    Authors: Zhuoyi Huang, Navin Rustagi, Narayanan Veeraraghavan, Andrew Carroll, Richard Gibbs, Eric Boerwinkle, Manjunath Gorentla Venkata and Fuli Yu

    Citation: BMC Bioinformatics 2016 17:361

    Content type: Methodology article

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  38. One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PT...

    Authors: Thammakorn Saethang, D. Michael Payne, Yingyos Avihingsanon and Trairak Pisitkun

    Citation: BMC Bioinformatics 2016 17:307

    Content type: Research article

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