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

2. 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
August 2008
Bioinformatics Tools for Comparative Genomics of Vectors

3. 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.
August 2008
Bioinformatics Tools for Comparative Genomics of Vectors

4. 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
August 2008
Bioinformatics Tools for Comparative Genomics of Vectors

5. 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
August 2008
Bioinformatics Tools for Comparative Genomics of Vectors

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