Bioinformatics Tools for Comparative Genomics of Vectors

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Presentation transcript:

Bioinformatics Tools for Comparative Genomics of Vectors Genome Browsers August 2008 Bioinformatics Tools for Comparative Genomics of Vectors

Bioinformatics Tools for Comparative Genomics of Vectors 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/ August 2008 Bioinformatics Tools for Comparative Genomics of Vectors

Bioinformatics Tools for Comparative Genomics of Vectors 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 August 2008 Bioinformatics Tools for Comparative Genomics of Vectors

Bioinformatics Tools for Comparative Genomics of Vectors 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 August 2008 Bioinformatics Tools for Comparative Genomics of Vectors

Bioinformatics Tools for Comparative Genomics of Vectors 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 August 2008 Bioinformatics Tools for Comparative Genomics of Vectors

Bioinformatics Tools for Comparative Genomics of Vectors Artemis exercises August 2008 Bioinformatics Tools for Comparative Genomics of Vectors