Rice Multi-platform Microarrary Search

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:

  1. TIGR Rice Genome Annotation v5 cDNAs
  2. Rice full-length cDNAs
  3. TIGR Plant Transcript Assemblies
  4. 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)