Note: the cross-platform searches have not yet been updated to incorporate Release 5 annotation of the Rice Annotation Project.
The Rice Multi-platform Search page is a tool that allows users the ability to search across five different rice oligo microarray platform types (Affymetrix, Agilent, BGI/Yale, NSF-20K,NSF-45K) to determine which probes from each platform map to a common a gene target.
To determine which probes from each platform mapped to a specific target, each probe was searched against a successive series of nucleotide/protein databases to find if that particular oligo mapped to any targets at 100% coverage and 100% identity. If there was a match, that probe was considered to be mapped and removed as a list of candidates to be searched against in the following round of database searches.
The databases used were as follows:
- TIGR Rice Genome Annotation v5 cDNAs
- Rice full-length cDNAs
- TIGR Plant Transcript Assemblies
- TIGR Rice Genome Annotation pseudomolecules
Alignment searches were conducted using blat. In the case of the Affymetrix searches, a probe set was considered to have been mapped if the entire set of 11 designed probes (8-10 in some cases) aligned with 100% identity and coverage.
To use this search, submit a file containing a list of identifiers of interest using the file browser menu (max 1000 identifiers, one per line). Or, paste directly into the search box a list of indentifiers. Select the output type that is desired (html or tab-delimited plain text) and click ‘Submit’.
Example identifiers include:
- LOC_Os12g17910.1 (TIGR Rice Genome Annotation cDNA)
- AK058910 (Rice full-length cDNA)
- TA61684_4530 (Rice Transcript Assembly)
- TR011789 (NSF Rice Oligonucleotide Microarray 20K ID)
- TR062199 (NSF Rice Oligonucleotide Microarray 45K ID)
- Os.17916.2.A1_a_at (Affymetrix Probe Set ID)
- Os026376_01 (BGI/Yale ID)
- A_71_P117054 (Agilent ID)
The entire probe mapping matrix table is available for download:
rice_matrix_table.mar1307.zip Rice Multi-platform Table (zip, 942K)