Information on Data Versioning

Overview

All data, analyses and tools from the Solanaceae Genomics Resource project that rely on public source data are updated on at least a quarterly basis (where appropriate).

Current Release

The Solanaceae Genomics Resource is currently on Release 3.

Genomic datasets used in annotation and analysis prepared for this release were retrieved from GenBank on or around 2008-12-18.

The following PlantGDB PUTs versions were used for this release:

SpeciesVersion
Capsicum annuum157a
Nicotiana benthamiana161a
Nicotiana langsdorffii x Nicotiana sanderae157a
Nicotiana sylvestris163a
Nicotiana tabacum169a
Petunia x hybrida159a
Solanum chacoense163a
Solanum habrochaites163a
Solanum lycopersicum161a
Solanum pennellii163a
Solanum tuberosum157a

BLAST Databases

The following sequence databases are currently available for searching through our BLAST tool.

Nucleotide Databases

Genomic

Potato BACs
Database is updated weekly with current data obtained from GenBank.
Potato Chr. 6 BACs (RHPOTKEY)
BACs from the PGSC RHPOTKEY library. Database is updated weekly with current data obtained from GenBank.
Potato BAC Ends
Database is updated weekly with current data obtained from GenBank.
Tobacco 454 BACs
Current public data release from the Tobacco Genome Initiative.
Tobacco Sheared BACs
Current public data release from the Tobacco Genome Initiative.
Tobacco Methyl-Filtered CAP3 Assemblies
Current public data release from the Tobacco Genome Initiative.
Tomato BACs
Database is updated weekly with current data obtained from GenBank.
Tomato BAC Ends
Database is updated weekly with current data obtained from GenBank.
Solanaceae BACs (all species)
Database is updated weekly with current data obtained from GenBank.
Solanum tuberosum BACs
Database is updated weekly with current data obtained from GenBank.
Solanum lycopersicum BACs
Database is updated weekly with current data obtained from GenBank.
Solanum bulbocastanum BACs
Database is updated weekly with current data obtained from GenBank.
Solanum demissum BACs
Database is updated weekly with current data obtained from GenBank.
Solanum melongena BACs
Database is updated weekly with current data obtained from GenBank.
Solanum pimpinellifolium BACs
Database is updated weekly with current data obtained from GenBank.
Capsicum annuum BACs
Database is updated weekly with current data obtained from GenBank.
Capsicum frutescens BACs
Database is updated weekly with current data obtained from GenBank.
Nicotiana tabacum BACs
Database is updated weekly with current data obtained from GenBank.
Nicotiana sylvestris BACs
Database is updated weekly with current data obtained from GenBank.
Nicotiana tomentosiformis BACs
Database is updated weekly with current data obtained from GenBank.
Petunia integrifolia subsp. inflata BACs
Database is updated weekly with current data obtained from GenBank.
Atropa belladonna BACs
Database is updated weekly with current data obtained from GenBank.

Transcriptomic

Solanaceae BAC MAKER Transcripts
Transcripts from all Solanaceae BACs predicted using the MAKER annotation pipeline
Tobacco Sheared BACs MAKER-predicted transcripts
Transcripts predicted using MAKER on current public data release from the Tobacco Genome Initiative.
Tobacco 454 BACs MAKER-predicted transcripts
Transcripts predicted using MAKER on current public data release from the Tobacco Genome Initiative.
Solanaceae PUTs (all species)
PlantGDB-assembled Unique Transcripts (PUTs) from all species in the Solanaceae. PUTs version consisent with those used in annotation and analysis (see table above).
Solanum tuberosum PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Solanum lycopersicum PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Nicotiana tabacum PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Capsicum annuum PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Nicotiana benthamiana PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Nicotiana langsdorffii x Nicotiana sanderae PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Nicotiana sylvestris PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Petunia x hybrida PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Solanum chacoense PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Solanum habrochaites PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).
Solanum pennellii PUTs
PUTs version consisent with those used in annotation and analysis for current release (see table above).

Polypeptide Databases

Solanaceae BAC MAKER Proteins
Proteins from all Solanaceae BACs predicted using the MAKER annotation pipeline
Tobacco Sheared BACs MAKER-predicted proteins
Proteins predicted using MAKER on current public data release from the Tobacco Genome Initiative.
Tobacco 454 BACs MAKER-predicted proteins
Proteins predicted using MAKER on current public data release from the Tobacco Genome Initiative.
TAIR Arabidopsis Proteome Release 8
The current release of the Arabidopsis proteome obtained from TAIR
Grape Proteome v1
The current release of the Grape proteome obtained from Genoscope
Poplar Proteome v1.1
The current release of the Poplar proteome obtained from JGI