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BMC Bioinformatics

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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2016 Journal Metrics

  • Citation Impact
    2.448 - 2-year Impact Factor
    3.450 - 5-year Impact Factor
    0.946 - Source Normalized Impact per Paper (SNIP)
    1.467 - SCImago Journal Rank (SJR)

    1405 Usage Factor

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