Genome, EST and other sequence databases

BOGAS genome annotation editor

ITAG aims at providing the best possible genome annotation. Still, errors can occur. The BOGAS interface offers preprocessed data and access to tools that allow experts to correct the predictions. These include JalView and GenomeView. Contact beg-bogas[at]psb.ugent.be for a login.

EUSOL tomato genome database

August 2010: Pre-release VERSION 2.30 of the assembled draft genome sequence of Solanum lycopersicum cv. Heinz 1706 available This tomato genome database is still under development. Currently, it only contains PRELIMINARY data which is mainly useful for the tomato genome sequencing consortium. The annotations presented here (ITAG v1.0) are NOT yet in a final state. More data will be included in the near future.

Isola - an italian solanaceae genomics resource

ISOL@ is currently organized into two main levels: the genome and the expression levels. The cornerstone of the genome level is represented by the tomato genome draft sequences. The founding elements of the expression level are the Solanaceae EST collections and the oligonucleotide probe-sets which have been generated for the production of the tomato expression microarrays. A nonstop crosstalk between the levels is based on the data source sharing and on the integration of the information which belongs to the respective under parts. Each level can be independently accessed through specific Web interfaces which allow user-driven data investigation.

Potato genome Gbrowse

A Gbrowse installation for the Solanum phureja DM1-3 516R44 (CIP801092) Genome and annotation by the Potato Genome Sequencing Consortium.

SGN (Cornell)

The SOL Genomics Network is a Clade Oriented Database (COD) containing genomic, genetic and taxonomic information for species in the Euasterid clade, including the families Solanaceae (e.g. tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to the fully-sequenced Arabidopsis genome.

SGN Gbrowse for ITAG v2

 

SGN tomato genome resources

Resources for the tomato genome at Solgenomics Network, including access to sequences (BACs, contigs, scaffolds, different assembly versions) and annotation, including the Gbrowse genome browser.

SOLESTdb (Unina)

This database has been designed to manage and to explore the huge amount of EST reads from 14 Solanaceae and 2 Rubiaceae species. The SOLEST database is constructed by first clustering (EST reads are searched pairwise against each other and grouped into clusters based on shared sequence similarity), then assembling EST reads to produce tentative consensus sequences (TCs) and singletons (sESTs). The total number of unique transcripts found are annotated and classified according to their biological functions.

Solgenomics.net (SGN) mirror at WUR

A mirror of the solgenomics network database is now mirrored at Wageningen UR Plant Breeding.