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      Is Open Access

      BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Background

          The wide range of potential applications has made the Basic Local Alignment Search Tool (BLAST) a ubiquitous tool in the field of Molecular Biology. Within this context, it is increasingly appealing to embed BLAST services within larger Web applications.

          Results

          This work introduces BlasterJS viewer, a new JavaScript library for the lightweight development of Web-based applications supporting the visualisation of BLAST outputs. BlasterJS detaches from similar data viewers by focusing on the visual and interactive display of sequence similarity results and being completely independent of BLAST services. BlasterJS is compatible with the text outputs generated by the BLAST family of programs, namely BLASTp, BLASTn, BLASTx, tBLASTn, and tBLASTx, and works in all major Web browsers. Furthermore, BlasterJS is available through the EBI’s BioJS registry 5, which extends its potential use to a wider scope of bioinformatics applications.

          Conclusions

          BlasterJS is new Javascript library that enables easy and seamless integration of visual and interactive representations of BLAST outputs in Web-based applications supporting sequence similarity search. BlasterJS is free accessible at http://sing-group.org/blasterjs/.

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          Most cited references 10

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          Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

           S Altschul (1997)
          The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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            ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets.

            ViroBLAST is a stand-alone BLAST web interface for nucleotide and amino acid sequence similarity searches. It extends the utility of BLAST to query against multiple sequence databases and user sequence datasets, and provides a friendly output to easily parse and navigate BLAST results. ViroBLAST is readily useful for all research areas that require BLAST functions and is available online and as a downloadable archive for independent installation. http://indra.mullins.microbiol.washington.edu/blast/viroblast.php.
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              BioJS: an open source JavaScript framework for biological data visualization.

              BioJS is an open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes a collection of components purposely designed to require a very simple configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community. http://code.google.com/p/biojs/. Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                Role: SoftwareRole: ValidationRole: Writing – original draft
                Role: Formal analysisRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: MethodologyRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: MethodologyRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                9 October 2018
                2018
                : 13
                : 10
                Affiliations
                [1 ] ESEI - Department of Computer Science, University of Vigo, Ourense, Spain
                [2 ] CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Vigo, Spain
                [3 ] Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Villaviciosa, Asturias, Spain
                [4 ] SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
                [5 ] CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
                UMR-S1134, INSERM, Université Paris Diderot, INTS, FRANCE
                Author notes

                Competing Interests: Borja Sánchez is on the scientific board and is co-founder of Microviable Therapeutics SL. The other authors have no competing interests. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

                Article
                PONE-D-18-15700
                10.1371/journal.pone.0205286
                6177166
                30300406
                © 2018 Blanco-Míguez et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Page count
                Figures: 5, Tables: 1, Pages: 10
                Product
                Funding
                Funded by: Spanish “Programa Estatal de Investigación, Desarrollo e Inovación Orientada a los Retos de la Sociedad”
                Award ID: AGL2013-44039R
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002704, Fundación Científica Asociación Española Contra el Cáncer;
                Award ID: "Obtención de pépti-dos bioactivos contra el Cáncer Colo-Rectal a partir de secuencias genéticas de microbiomas intestinales", grant PS-2016
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001871, Fundação para a Ciência e a Tecnologia;
                Award ID: strategic funding of UID/BIO/04469/2013 unit
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001871, Fundação para a Ciência e a Tecnologia;
                Award ID: COMPETE 2020 (POCI-01-0145-FEDER-006684)
                Award Recipient :
                Funded by: CITI (Centro de Investigación, Transferencia e Innovación (ES)
                Award Recipient :
                This work was supported by the Spanish “Programa Estatal de Investigación, Desarrollo e Inovación Orientada a los Retos de la Sociedad” (grant AGL2013-44039R to BS and AL); and the Asociación Española Contra el Cancer ("Obtención de pépti-dos bioactivos contra el Cáncer Colo-Rectal a partir de secuencias genéticas de microbiomas intestinales", grant PS-2016 to BS and ABM). This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit (AL) and COMPETE 2020 (POCI-01-0145-FEDER-006684 to AL). SING group thanks CITI (Centro de Investigación, Trans-ferencia e Innovación) from University of Vigo for hosting its IT infrastructure. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Research and analysis methods
                Database and informatics methods
                Bioinformatics
                Sequence analysis
                BLAST algorithm
                Research and Analysis Methods
                Database and Informatics Methods
                Database Searching
                Sequence Similarity Searching
                Computer and Information Sciences
                Computer Applications
                Web-Based Applications
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Alignment
                Research and Analysis Methods
                Computational Techniques
                Split-Decomposition Method
                Multiple Alignment Calculation
                Research and Analysis Methods
                Database and Informatics Methods
                Biological Databases
                Sequence Databases
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Databases
                Engineering and Technology
                Human Factors Engineering
                Man-Computer Interface
                Graphical User Interfaces
                Computer and Information Sciences
                Computer Architecture
                User Interfaces
                Graphical User Interfaces
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Sequencing Techniques
                Protein Sequencing
                Research and Analysis Methods
                Molecular Biology Techniques
                Sequencing Techniques
                Protein Sequencing
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

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