Gramene

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Release Notes

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