Agilent Barley Gene Expression Microarray Reannotation

After downloading the full sequences of the array oligos from the Core and EST sections of the NCBI Nucleotide Archive, the TIGR Plant Transcript Assembly and the DFCI Gene Indices collection, which were not provided with the array annotation, a search was made for possible homologs in the 2 February 2011 UniProt Knowledgebase Plant section and the Gramene rice genome assembly, version MSU6.

A BLAST search was run with default parameters, the only modification being the use of the query sequence filtering for low complexity regions. After the BLAST search, the results were filtered, choosing the one with the best score, but requiring an e-value lower than 1e-30 and an overall fraction of iden- tical positions across the hit and query alignment of at least 50%. The description and GeneOntology (GO) associations were reannotated for all array oligos where a suitable homolog was found either in UniProt or in the Gramene database.