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      Web Apollo: a web-based genomic annotation editing platform

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          Abstract

          Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.

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          The zebrafish reference genome sequence and its relationship to the human genome.

          Kerstin Howe, Matthew D. Clark, Carlos F Torroja … (2013)
          Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.
          Article 0 comments Cited 1442 times – based on 0 reviews     Review now
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            Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

            Jeremy Goecks, Anton Nekrutenko, James E. Taylor (2010)
            Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.
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              BigWig and BigBed: enabling browsing of large distributed datasets

              W. J. Kent, A. S. Zweig, Lisa Barber … (2010)
              Summary: BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets. Availability and implementation: Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu Contact: ann@soe.ucsc.edu Supplementary information: Supplementary byte-level details of the BigWig and BigBed file formats are available at Bioinformatics online. For an in-depth description of UCSC data file formats and custom tracks, see http://genome.ucsc.edu/FAQ/FAQformat.html and http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
              Article 0 comments Cited 579 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Eduardo Lee
                Gregg A Helt
                Justin T Reese
                Monica C Munoz-Torres
                Chris P Childers
                Robert M Buels
                Lincoln Stein
                Ian H Holmes
                Christine G Elsik
                Suzanna E Lewis
                Journal
                Journal ID (nlm-ta): Genome Biol
                Journal ID (iso-abbrev): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2013
                Publication date (Electronic): 30 August 2013
                Volume: 14
                Issue: 8
                Page: R93
                Affiliations
                [1 ]Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
                [2 ]Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
                [3 ]Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
                [4 ]Ontario Institute of Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3
                [5 ]Department of Molecular Genetics, University of Toronto, 172 St. George Street Toronto, Ontario, Canada M5R 0A3
                [6 ]Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
                Article
                Publisher ID: gb-2013-14-8-r93
                DOI: 10.1186/gb-2013-14-8-r93
                PMC ID: 4053811
                PubMed ID: 24000942
                SO-VID: c933193e-c712-4bba-8ce0-087a85961f69
                Copyright © Copyright © 2013 Lee et al.; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 10 May 2013
                Date revision received : 23 August 2013
                Date accepted : 30 August 2013
                Categories
                Subject: Software

                ScienceOpen disciplines: Genetics
                Keywords: genome,collaborative,editor
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: genome, collaborative, editor

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