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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:
The entire probe mapping matrix table is available for download:

rice_matrix_table.mar1307.zip Rice Multi-platform Table (zip, 942K)



Enter the name of the file containing a list of identifiers (max 1000 identifiers, one per line).



OR

Enter a list of identifier terms in the text area below (max 1000 identifiers, one per line).



Return results as HTML Plain text

  




                                               





Last modified: Wednesday, 18-Jun-2008 11:37:34 EDT