Agilent provides annotation for its gene expression probes using BLAST and/or BLAT to align probes to various database transcripts. For more information on these sequence alignment tools, go to www.ncbi.nih.gov/BLAST/ and www.genomeblat.com. The exact procedure depends on the species.
Each probe is annotated to a primary transcript and secondary transcripts to assist you in probe searches.
After the transcript alignments are established, Agilent uses public domain linkages from the transcript identifiers to derive additional annotations such as title lines, gene names, gene symbols, or Gene Ontology terms. The additional annotations are derived from the primary transcript whenever possible, and from the secondary transcripts if unavailable from the primary.
Agilent computes genomic annotation for each probe by aligning the primary transcripts to the genome using BLAT, aligning the probes to the transcripts, and subsequently computing the probe alignment to the genome. Agilent employs this multi-step process to provide greater robustness when a probe spans a splice site.
See also
Annotation changes
How to monitor annotation changes
View probe annotations