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. Software

    Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data

    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...

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

    BMC Bioinformatics 2017 18:305

    Published on: 17 June 2017

  2. Research Article

    A systematic evaluation of nucleotide properties for CRISPR sgRNA design

    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...

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

    BMC Bioinformatics 2017 18:297

    Published on: 6 June 2017

  3. Software

    ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins

    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 ...

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

    BMC Bioinformatics 2017 18:233

    Published on: 2 May 2017

  4. Software

    QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

    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...

    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

    BMC Bioinformatics 2017 18:225

    Published on: 28 April 2017

  5. Database

    MYCbase: a database of functional sites and biochemical properties of Myc in both normal and cancer cells

    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...

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

    BMC Bioinformatics 2017 18:224

    Published on: 28 April 2017

  6. Software

    Segmentum: a tool for copy number analysis of cancer genomes

    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,...

    Ebrahim Afyounian, Matti Annala and Matti Nykter

    BMC Bioinformatics 2017 18:215

    Published on: 13 April 2017

  7. Research article

    Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis

    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...

    Gaurang Mahajan and Shekhar C. Mande

    BMC Bioinformatics 2017 18:201

    Published on: 4 April 2017

  8. Research article

    DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins

    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...

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

    BMC Bioinformatics 2017 18:190

    Published on: 24 March 2017

  9. Software

    TreeToReads - a pipeline for simulating raw reads from phylogenies

    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...

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

    BMC Bioinformatics 2017 18:178

    Published on: 20 March 2017

  10. Software

    LW-FQZip 2: a parallelized reference-based compression of FASTQ files

    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...

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

    BMC Bioinformatics 2017 18:179

    Published on: 20 March 2017

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