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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. Large sequence datasets are difficult to visualize and handle. Additionally, they often do not represent a random subset of the natural diversity, but the result of uncoordinated and convenience sampling. Cons...

    Authors: Fabrizio Menardo, Chloé Loiseau, Daniela Brites, Mireia Coscolla, Sebastian M. Gygli, Liliana K. Rutaihwa, Andrej Trauner, Christian Beisel, Sonia Borrell and Sebastien Gagneux

    Citation: BMC Bioinformatics 2018 19:164

    Content type: Software

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  2. In the last decade and a half it has been firmly established that a large number of proteins do not adopt a well-defined (ordered) structure under physiological conditions. Such intrinsically disordered protei...

    Authors: Nenad S. Mitić, Saša N. Malkov, Jovana J. Kovačević, Gordana M. Pavlović-Lažetić and Miloš V. Beljanski

    Citation: BMC Bioinformatics 2018 19:158

    Content type: Research article

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  3. Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and a...

    Authors: Krittima Anekthanakul, Apiradee Hongsthong, Jittisak Senachak and Marasri Ruengjitchatchawalya

    Citation: BMC Bioinformatics 2018 19:149

    Content type: Database

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  4. The study of the huge diversity of immune receptors, often referred to as immune repertoire profiling, is a prerequisite for diagnosis, prognostication and monitoring of hematological disorders. In the era of ...

    Authors: Christos Maramis, Athanasios Gkoufas, Anna Vardi, Evangelia Stalika, Kostas Stamatopoulos, Anastasia Hatzidimitriou, Nicos Maglaveras and Ioanna Chouvarda

    Citation: BMC Bioinformatics 2018 19:144

    Content type: Software

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  5. After decades of identifying risk factors using array-based genome-wide association studies (GWAS), genetic research of complex diseases has shifted to sequencing-based rare variants discovery. This requires l...

    Authors: Yingxue Ren, Joseph S. Reddy, Cyril Pottier, Vivekananda Sarangi, Shulan Tian, Jason P. Sinnwell, Shannon K. McDonnell, Joanna M. Biernacka, Minerva M. Carrasquillo, Owen A. Ross, Nilüfer Ertekin-Taner, Rosa Rademakers, Matthew Hudson, Liudmila Sergeevna Mainzer and Yan W. Asmann

    Citation: BMC Bioinformatics 2018 19:139

    Content type: Research article

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  6. High quality functional annotation is essential for understanding the phenotypic consequences encoded in a genome. Despite improvements in bioinformatics methods, millions of sequences in databanks are not ass...

    Authors: Jonathan Mercier, Adrien Josso, Claudine Médigue and David Vallenet

    Citation: BMC Bioinformatics 2018 19:132

    Content type: Methodology article

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  7. Single nucleotide polymorphisms (SNPs) located within the human genome have been shown to have utility as markers of identity in the differentiation of DNA from individual contributors. Massively parallel DNA ...

    Authors: M. Heath Farris, Andrew R. Scott, Pamela A. Texter, Marta Bartlett, Patricia Coleman and David Masters

    Citation: BMC Bioinformatics 2018 19:126

    Content type: Research article

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  8. Genome-wide association studies (GWASs) have been widely used to discover the genetic basis of complex phenotypes. However, standard single-SNP GWASs suffer from lack of power. In particular, they do not direc...

    Authors: Christine Sinoquet

    Citation: BMC Bioinformatics 2018 19:106

    Content type: Methodology Article

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  9. Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by model...

    Authors: Andrey Ziyatdinov, Miquel Vázquez-Santiago, Helena Brunel, Angel Martinez-Perez, Hugues Aschard and Jose Manuel Soria

    Citation: BMC Bioinformatics 2018 19:68

    Content type: Software

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  10. Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep se...

    Authors: Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni and Stefan Bonn

    Citation: BMC Bioinformatics 2018 19:54

    Content type: Software

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  11. The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of databases containing sequence data for hundreds of thousands influenza strai...

    Authors: Christopher S. Anderson, Patrick R. McCall, Harry A. Stern, Hongmei Yang and David J. Topham

    Citation: BMC Bioinformatics 2018 19:51

    Content type: Research Article

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  12. The advent of modern high-throughput genetics continually broadens the gap between the rising volume of sequencing data, and the tools required to process them. The need to pinpoint a small subset of functiona...

    Authors: Monika Mozere, Mehmet Tekman, Jameela Kari, Detlef Bockenhauer, Robert Kleta and Horia Stanescu

    Citation: BMC Bioinformatics 2018 19:46

    Content type: Software

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  13. The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly acces...

    Authors: Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart and Paul C. Boutros

    Citation: BMC Bioinformatics 2018 19:28

    Content type: Research Article

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  14. Protein or nucleic acid sequences contain a multitude of associated annotations representing continuous sequence elements (CSEs). Comparing these CSEs is needed, whenever we want to match identical annotations...

    Authors: Roman Prytuliak, Friedhelm Pfeiffer and Bianca Hermine Habermann

    Citation: BMC Bioinformatics 2018 19:24

    Content type: Methodology Article

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  15. Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results ...

    Authors: Jordi Martorell-Marugan, Daniel Toro-Dominguez, Marta E. Alarcon-Riquelme and Pedro Carmona-Saez

    Citation: BMC Bioinformatics 2017 18:563

    Content type: Software

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  16. High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number ...

    Authors: Kenneth D. Doig, Jason Ellul, Andrew Fellowes, Ella R. Thompson, Georgina Ryland, Piers Blombery, Anthony T. Papenfuss and Stephen B. Fox

    Citation: BMC Bioinformatics 2017 18:555

    Content type: Software

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  17. Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in...

    Authors: Matthias Beyens, Nele Boeckx, Guy Van Camp, Ken Op de Beeck and Geert Vandeweyer

    Citation: BMC Bioinformatics 2017 18:554

    Content type: Software

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  18. Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent ...

    Authors: Megan J. Bowman, Jane A. Pulman, Tiffany L. Liu and Kevin L. Childs

    Citation: BMC Bioinformatics 2017 18:522

    Content type: Methodology Article

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  19. Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic...

    Authors: Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang and David Vocadlo

    Citation: BMC Bioinformatics 2017 18:521

    Content type: Software

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  20. Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene thera...

    Authors: Giulio Spinozzi, Andrea Calabria, Stefano Brasca, Stefano Beretta, Ivan Merelli, Luciano Milanesi and Eugenio Montini

    Citation: BMC Bioinformatics 2017 18:520

    Content type: Software

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  21. With the plummeting cost of the next-generation sequencing technologies, high-density genetic linkage maps could be constructed in a forest hybrid F1 population. However, based on such genetic maps, quantitative ...

    Authors: Fenxiang Liu, Chunfa Tong, Shentong Tao, Jiyan Wu, Yuhua Chen, Dan Yao, Huogen Li and Jisen Shi

    Citation: BMC Bioinformatics 2017 18:515

    Content type: Software

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  22. Gene set enrichment analysis and overrepresentation analyses are commonly used methods to determine the biological processes affected by a differential expression experiment. This approach requires biologicall...

    Authors: Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan and Casey S. Greene

    Citation: BMC Bioinformatics 2017 18:512

    Content type: Methodology Article

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  23. Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, whil...

    Authors: Kosai Al-Nakeeb, Thomas Nordahl Petersen and Thomas Sicheritz-Pontén

    Citation: BMC Bioinformatics 2017 18:510

    Content type: Software

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  24. Nowadays, many public repositories containing large microarray gene expression datasets are available. However, the problem lies in the fact that microarray technology are less powerful and accurate than more ...

    Authors: Daniel Castillo, Juan Manuel Gálvez, Luis Javier Herrera, Belén San Román, Fernando Rojas and Ignacio Rojas

    Citation: BMC Bioinformatics 2017 18:506

    Content type: Research Article

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  25. 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

    Content type: Software

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  26. 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

    Content type: Software

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  27. 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

    Content type: Database

    Published on:

  28. 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

    Content type: Research Article

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  29. 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

    Content type: Software

    Published on:

  30. 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

    Content type: Software

    Published on:

  31. 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

    Content type: Software

    Published on:

  32. 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

    Content type: Software

    Published on:

  33. 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

    Content type: Research Article

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  34. 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

    Content type: Database

    Published on:

  35. 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

    Content type: Research Article

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  36. 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

    Content type: Software

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  37. 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

    Content type: Research Article

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  38. 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

    Content type: Software

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  39. 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

    Content type: Software

    Published on:

  40. 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

    Content type: Software

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  41. 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

    Content type: Methodology Article

    Published on:

  42. 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

    Content type: Methodology Article

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