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Genome Browsers

Genome Browsers. Artemis. Annotation platform used by Sanger Institute Pathogen group Can be used as a visualization tool Capable of reading EMBL/GenBank and GFF files Built in database entry fetching facility Designed for bacterial genomes Used for small eukaryotes

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Genome Browsers

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  1. Genome Browsers Bioinformatics Tools for Comparative Genomics of Vectors

  2. Artemis • Annotation platform used by Sanger Institute Pathogen group • Can be used as a visualization tool • Capable of reading EMBL/GenBank and GFF files • Built in database entry fetching facility • Designed for bacterial genomes • Used for small eukaryotes • Limited use for larger, heavily spliced genomes http://www.sanger.ac.uk/Software/Artemis/v10/ Bioinformatics Tools for Comparative Genomics of Vectors

  3. GBrowse • Developed by Lincoln Stein (CSHL/Toronto) • Very flexible • Works with flat files, GFF databases, CHADO RDBs and via adaptors from EMBL/GenBank files • Users include PlasmoDB, FlyBase and WormBase. http://gmod.org/wiki/index.php/Gbrowse Bioinformatics Tools for Comparative Genomics of Vectors

  4. Ensembl • Bespoke browser from the Ensembl group • Many different display pages for a variety of data types • Users include Ensembl, VectorBase, Gramene http://www.ensembl.org/index.html Bioinformatics Tools for Comparative Genomics of Vectors

  5. Apollo • Annotation platform used by FlyBase and TAIR groups. • Developed through Berkeley/EBI/GMOD. • Can be used as a visualization tool • Capable of reading CHADO-XML and GFF files • Adaptors for CHADO RDB and Ensembl databases http://gmod.org/wiki/index.php/Apollo Bioinformatics Tools for Comparative Genomics of Vectors

  6. Artemisexercises Bioinformatics Tools for Comparative Genomics of Vectors

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