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. Research Article

    Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family

    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 ...

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

    BMC Bioinformatics 2017 18:439

    Published on: 3 October 2017

  2. Software

    Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data

    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...

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

    BMC Bioinformatics 2017 18:436

    Published on: 3 October 2017

  3. Software

    SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees

    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...

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

    BMC Bioinformatics 2017 18:433

    Published on: 30 September 2017

  4. Software

    VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences

    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 ...

    Duo Xu, Yousef Jaber, Pavlos Pavlidis and Omer Gokcumen

    BMC Bioinformatics 2017 18:426

    Published on: 26 September 2017

  5. Software

    VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy

    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...

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

    BMC Bioinformatics 2017 18:421

    Published on: 20 September 2017

  6. Research Article

    Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis

    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...

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

    BMC Bioinformatics 2017 18:401

    Published on: 7 September 2017

  7. Database

    A new and updated resource for codon usage tables

    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...

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

    BMC Bioinformatics 2017 18:391

    Published on: 2 September 2017

  8. Research Article

    Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains

    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 ...

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

    BMC Bioinformatics 2017 18:370

    Published on: 16 August 2017

  9. Research Article

    Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility

    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...

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

    BMC Bioinformatics 2017 18:355

    Published on: 27 July 2017

  10. Software

    Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications

    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...

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

    BMC Bioinformatics 2017 18:344

    Published on: 19 July 2017

  11. Methodology Article

    ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data

    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...

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

    BMC Bioinformatics 2017 18:330

    Published on: 10 July 2017

  12. Software

    SparkBLAST: scalable BLAST processing using in-memory operations

    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...

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

    BMC Bioinformatics 2017 18:318

    Published on: 27 June 2017

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