Rice Array Element Search

To determine which probes from each platform mapped to a specific target, each probe was searched against a successive series of nucleotide 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. MSU/TIGR Rice Genome Annotation v6 cDNAs
  2. RAP3 Rice Genome Annotation cDNAs
  3. Rice KOME full-length cDNAs

Alignment searches were conducted using NCBI BLAST. In the case of the Affymetrix searches, a probe set was considered to have been mapped if more than half of the entire set of designed probes aligned with 100% identity and coverage.

Download the whole rice array elements information (zip, 7M) (Updated April, 2011).

The data types in the Rice Array Element Search are the following:

Array Element ID: a unique identifier generated by manufacture to reference this probe.

Array Platform: The array platform containing this probe: Affymetrix, Agilent 22K, Agilent 44K, BGI/Yale, NSF 20K and NSF 45K (23K A or 23K B).

Matched Gene ID: The sequence this probe aligns to at 100% length and identity. Example match IDs include MSU/TIGR Rice Genome Annotation release 6 models (e.g. LOC_Os01g01010.1), RAP3 (e.g. Os01t0100100-01) and full length cDNAs (e.g. AK058204).

Probe Sequence: The sequence of the probe.

Last modified: Friday, 30-Mar-2012 07:42:04 PDT