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Release Notes March 2005

New Genomes Data;

• Import of the TIGR pseudomolecule assembly release 3 of IRGSP finished sequence, and associated gene model predictions.


• Annotation of the TIGR gene models with protein domains, generated using InterproScan. Annotations include;
• Interpro domains,
• Pfam domains,
• SMART domains,
• PROSITE profiles,
• PROSITE Patterns,
• SUPERFAMILY families,
• ProDom domains,
• PIR SuperFamily families,
• TIGRFAM families,
• PRINTS motifs,
• Coil domans,
• Low complexity (seg) regions.


• GO terms associated with the above domains have been mapped to the TIGR gene model transcripts.


• Addition of gene models predicted by the FGENESH Hidden Markov Model (HMM)-based ab-initio gene prediction program


• Addition of gene models submitted directly to GenBank in the form of nucleotide sequence annotations.


• Mapping to the Oryza sativa (japonica) genome of BAC end sequences generated by the OMAP project for the following species;
• Oryza alta,
• Oryza australiensis,
• Oryza glaberrima,
• Oryza punctata.


• Mapping to the Oryza sativa (japonica) genome of flanking sequence tags (FSTs);
• Rice T-DNA inserts,
• Rice Ds inserts.

New Genomes Features

• ContigView;
• Addition of tracks to display the new OMAP and FST mappings.
• Addition of an 'FST' configuration menu.


• TransView/ProtView;
• Addition of GO, Interpro and domain annotations to the display.


• DomainView;
• New page for the display of a given InterPro domain.


• BlastView;
• Addition of the new OMAP and FST data as searchable databases.


• Migration to Ensembl v28 code base and schema.

Release Notes Archive

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