Blast search was conducted with 22,746 GeneChip
target and probe sequences using an E-value cutoff of 0.000001.
Proper matches were established using the following criteria.
1. Using Affymetrix target sequences as query, we used these
criteria: (100% identity AND match length >= 50) OR (98% identity
AND match length equal to query length, i.e. the length of the
target sequence). Found the largest number of matches: 22132.
2. For those Affymetrix target sequences that had no match in
step 1 as query, we used these criteria: 98% identity, match length
>= 50. Found 231 matches.
3. For those Affymetrix target sequences that had no match in
step 1 or 2, we used these criteria: 98% identity, match length
>= 30. Found 19 matches.
4. For those target sequences producing no matches using the
above guidelines, the corresponding Affymetrix probe sequences
was used as the query, using the following criteria: (100% identity
AND match length >= 15) OR (98% identity AND match length equal
to query length, i.e. the length of the target sequence). Found
5. For those Affymetrix probe sequences without matches in step
4, all 11 probes were used for the blast with the same criteria
as above. Found 5 matches.
So the total number of matches from the blast above is 22609.
Comparison between the above result and Affymetrix's annotation
revealed that there are 139 genes having different AGI
numbers. When the AGI name changes in TIGR's database are taken
into account, however there are a total of 133 genes with
different AGI numbers.
The above blast result
can be found in the following files:
the annotation based on the above blast
the comparasion between the Affymetrix annotation and the TIGR
blast results. The AGI names of When a probe set has different
AGI numbers between Affymetrix annotation and TIGR blast result,
the AGI is tagged with "!!!-!!!".
the comparasion between Affy annotation with
*updated AGI names* and TIGR blast results.