ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Rice DB synchronises with MSU for TIGR LOC IDs (nuclear gene loci only) and retains historical and archival identifiers so that past papers can be analysed. See http://rice.plantbiology.msu.edu/​analyses_​nomenclature.shtml for the format.

Rice DB includes version 3.0, 5.0, 6.0, 6.1 and 7.0 model identifiers and point numbers from Michigan State University’s Rice Genome Annotation Project (MSU RGAP http://rice.plantbiology.msu.edu/). Sequences come from the International Rice Genome Sequencing Project (IRGSP http://rgp.dna.affrc.go.jp/IRGSP/), cultivar Nipponbare of Oryza sativa ssp. japonica.

From MSU’s website:

You can search either by legacy feature identifiers (e.g. 9638.m00152 or 11668.t00377) or MSU RGAP locus names (e.g. LOC_Os10g33200 or LOC_Os08g44450.3). Please note that not all gene models can be linked to models in other versions due to the genomic sequence changes when the rice genome is being finished and our pseudomolecules were constructed.
  • Feature identifiers and locus names are identical for releases 6 and 6.1.
  • Legacy feat names were dropped in release 7
  • Loci were only made obsolete in release 7. No new models were created in release 7
Usage When Searching Rice DB Usage Viewing Rice DB Results
  • Searching one TIGR ID with a point number will show a “flat file” info page (LOC_Os02g06480.1).
  • Searching for multiple TIGR IDs or IDs without point numbers will return a table of matching MSU loci.
  • Full text searches will find MSU putative function annotations.
  • Flat file info pages show all data considered by Rice DB.
  • TIGR IDs and version numbers are automatically shown in search results.
  • MSU annotations are automatically shown alongside full-text search results.
Example: LOC_Os02g06480
Example: LOC_Os06g03770.1
Example: loc_os02g06480.1, loc_os02g06480.2, loc_os02g06480.2
Example: get annotations, annotations array for LOC_Os02g06480.1, LOC_Os02g06480.1
Example: find TIGR identifiers for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
Example: find TIGR identifiers grouped for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
Example: find RAP identifiers grouped with ; for IDs like LOC_Os01g01010 LOC_Os02g52900.1
Example: find RAP identifiers grouped with ' & ' for IDs like LOC_Os01g01010 LOC_Os02g52900.1
Example: get distinct TIGR identifiers for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
Example: get unique sorted list of TIGR identifiers for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
Example: find duplicate TIGR identifiers for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
Example: find duplicates in TIGR identifiers for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
Example: find missing TIGR identifiers for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
Example: find unknown TIGR identifiers for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
Example: find unmatched TIGR identifiers for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
Example: find syntax errors in TIGR identifiers for IDs like Os01g0100100, Os01g0174900, Os01g0100100, asdfasdfn
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System Information

Transcript of last update

Took 59 seconds, 467 millis starting Sun, 24 Feb 2013 14:46:27 GMT:
Using /tmp/RiceDB/TIGR_
Using /var/www/ricedb/Data/downloaded/TIGR_
Adding MSU_CDS_COORDS column