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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. Content type: Software

    The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexe...

    Authors: Tao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo and Rui Zhang

    Citation: BMC Bioinformatics 2017 18:482

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  2. Content type: Software

    Large scale bacterial sequencing has made the determination of genetic relationships within large sequence collections of bacterial genomes derived from the same microbial species an increasingly common task. ...

    Authors: Oriol Mazariegos-Canellas, Trien Do, Tim Peto, David W. Eyre, Anthony Underwood, Derrick Crook and David H. Wyllie

    Citation: BMC Bioinformatics 2017 18:477

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  3. Content type: Database

    Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009...

    Authors: Oana Carja, Tongji Xing, Edward W. J. Wallace, Joshua B. Plotkin and Premal Shah

    Citation: BMC Bioinformatics 2017 18:461

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  4. Content type: Research Article

    Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene ...

    Authors: Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou and Kui Lin

    Citation: BMC Bioinformatics 2017 18:439

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  5. Content type: Software

    Copy number variations (CNVs) are the main genetic structural variations in cancer genome. Detecting CNVs in genetic exome region is efficient and cost-effective in identifying cancer associated genes. Many to...

    Authors: Jianing Gao, Changlin Wan, Huan Zhang, Ao Li, Qiguang Zang, Rongjun Ban, Asim Ali, Zhenghua Yu, Qinghua Shi, Xiaohua Jiang and Yuanwei Zhang

    Citation: BMC Bioinformatics 2017 18:436

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  6. Content type: Software

    Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the inter...

    Authors: Alan Beccati, Jan Gerken, Christian Quast, Pelin Yilmaz and Frank Oliver Glöckner

    Citation: BMC Bioinformatics 2017 18:433

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  7. Content type: Software

    Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has ...

    Authors: Duo Xu, Yousef Jaber, Pavlos Pavlidis and Omer Gokcumen

    Citation: BMC Bioinformatics 2017 18:426

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  8. Content type: Software

    The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the u...

    Authors: José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves, Pablo Marín-Garcia, Ignacio Medina, Vicente Arnau and Joaquín Dopazo

    Citation: BMC Bioinformatics 2017 18:421

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  9. Content type: Research Article

    Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition of lymphocyte populations. This opens the door for novel approaches to diagnose and pro...

    Authors: Jared Ostmeyer, Scott Christley, William H. Rounds, Inimary Toby, Benjamin M. Greenberg, Nancy L. Monson and Lindsay G. Cowell

    Citation: BMC Bioinformatics 2017 18:401

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  10. Content type: Database

    Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codo...

    Authors: John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V. Santana-Quintero, Upendra Katneni, Vahan Simonyan and Chava Kimchi-Sarfaty

    Citation: BMC Bioinformatics 2017 18:391

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  11. Content type: Research Article

    Discriminating driver mutations from the ones that play no role in cancer is a severe bottleneck in elucidating molecular mechanisms underlying cancer development. Since protein domains are representatives of ...

    Authors: Seirana Hashemi, Abbas Nowzari Dalini, Adrin Jalali, Ali Mohammad Banaei-Moghaddam and Zahra Razaghi-Moghadam

    Citation: BMC Bioinformatics 2017 18:370

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  12. Content type: Software

    Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS...

    Authors: Carlos Guzman and Iván D’Orso

    Citation: BMC Bioinformatics 2017 18:363

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  13. Content type: Research Article

    Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in vario...

    Authors: Sheng Liu, Cristina Zibetti, Jun Wan, Guohua Wang, Seth Blackshaw and Jiang Qian

    Citation: BMC Bioinformatics 2017 18:355

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  14. Content type: Software

    In mediation analysis if unmeasured confounding is present, the estimates for the direct and mediated effects may be over or under estimated. Most methods for the sensitivity analysis of unmeasured confounding...

    Authors: Sharon M. Lutz, Annie Thwing, Sarah Schmiege, Miranda Kroehl, Christopher D. Baker, Anne P. Starling, John E. Hokanson and Debashis Ghosh

    Citation: BMC Bioinformatics 2017 18:344

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  15. Content type: Software

    The increasing volume and complexity of high-throughput genomic data make analysis and prioritization of variants difficult for researchers with limited bioinformatics skills. Variant Ranker allows researchers to...

    Authors: John Alexander, Dimitris Mantzaris, Marianthi Georgitsi, Petros Drineas and Peristera Paschou

    Citation: BMC Bioinformatics 2017 18:341

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  16. Content type: Software

    Comparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to a reference genome, or two genomes to each other. The purpose of the comparison is u...

    Authors: Ksenia Khelik, Karin Lagesen, Geir Kjetil Sandve, Torbjørn Rognes and Alexander Johan Nederbragt

    Citation: BMC Bioinformatics 2017 18:338

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  17. Content type: Methodology Article

    Insecticide resistance is a substantial problem in controlling agricultural and medical pests. Detecting target site mutations is crucial to manage insecticide resistance. Though PCR-based methods have been wi...

    Authors: Dianhao Guo, Jiapeng Luo, Yuenan Zhou, Huamei Xiao, Kang He, Chuanlin Yin, Jianhua Xu and Fei Li

    Citation: BMC Bioinformatics 2017 18:330

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  18. Content type: Methodology Article

    Tn-Seq is a high throughput technique for analysis of transposon mutant libraries to determine conditional essentiality of a gene under an experimental condition. A special feature of the Tn-seq data is that m...

    Authors: Lili Zhao, Mark T. Anderson, Weisheng Wu, Harry L. T. Mobley and Michael A. Bachman

    Citation: BMC Bioinformatics 2017 18:326

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  19. Content type: Software

    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

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  20. Content type: Software

    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

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  21. Content type: Software

    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

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  22. Content type: Software

    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

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  23. Content type: Research Article

    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

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  24. Content type: Software

    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

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  25. Content type: Software

    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

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  26. Content type: Database

    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

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  27. Content type: Software

    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

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  28. Content type: Software

    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

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  29. Content type: Software

    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

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  30. Content type: Software

    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

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  31. Content type: Research article

    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

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  32. Content type: Research article

    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

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  33. Content type: Software

    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

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  34. Content type: Software

    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

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  35. Content type: Software

    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

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  36. Content type: Software

    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

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  37. Content type: Software

    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

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  38. Content type: Research article

    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

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  39. Content type: Software

    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

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  40. Content type: Software

    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

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  41. Content type: Research article

    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

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2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)


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