51
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Comparative Assembly Hubs: Web Accessible Browsers for Comparative Genomics

      Preprint

      Read this article at

      Bookmark
          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

          We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome in the collection, symmetrically. A new, intelligently scaled alignment display makes it simple to view all changes between the genomes at all levels of resolution, from substitutions to complex structural rearrangements, including duplications.

          Related collections

          Most cited references 1

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

          Summary: Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror. Availability and implementation: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu. Contact: donnak@soe.ucsc.edu
            Bookmark

            Author and article information

            Journal
            05 November 2013
            Article
            1311.1241

            http://arxiv.org/licenses/nonexclusive-distrib/1.0/

            Custom metadata
            10 pages, 3 figures
            q-bio.GN

            Genetics

            Comments

            Comment on this article