FC003 to Affymetrix probe-set files
Outline
Affymetrix microarrays can have more than one probe-set designed to a gene / transcript. To identify which Affymetrix probe-set closely matches your clone sequence, it is best to perform a probe match search of your sequence against either the Affymetrix probe-set or the parent sequences from which the Affymetrix probes were designed. BLAST searches can also be performed. You can download any of these sequences and perform probe match searches at the Affymetrix NetAffx Analysis Centre.
Affymetrix sequences
- Exemplar sequence: representative cDNA sequence for each gene / transcript derived from clustering into gene groups. Exemplar sequences usually have public accession codes.
- Consensus sequence: the end result from base-calling algorithms of aligned, clustered sequences. Consensus sequences have either an Affymetrix or a public accession code.
- Target sequence: sequence that was used for the design of the probe-sets
Probe match tool
Alignments by the probe match tool produce positive results only if every base in the probe sequence matches perfectly with those of the query sequence and do not have any gaps. This algorithm is therefore different to the BLAST algorithm. The probe match tool is best used to identify exact sequence matches. BLAST searches can be used to search for exact sequence matches or similarities.
