Primer name update

3-06 update

File containing updated gene names for the primer pairs: pcr.Primers.all.3-06.plus_gels.txt

Primer pair sequences: Primers.all.3-06.txt

Overall summary

Which PCR products changed names?

Changed 3540
Same 16064
PCR product doesn't contain a gene 867
No predicted PCR product 95

Primer pair gene names changes since the 4-02 version: 2557.

Gene coverage

Primer pairs match 16546 of 20068 Wormbase genes

Changes from previous primer->gene update:

Description of the Kim lab chip primer set

1323 Primers were poor and were re-made
1323 Re-made poor primers
17887 Primers made once
20533 total primer pairs

Previous primer name updates

The 4-02 version of the the update
The previous version of the the update
The third version of the the update
The second version of the the update
The first version of the the update

Decisions made in the analysis

1) 5 kb cutoff in PCR size used (few are over 2kb).

2) 50 bp overlap between a PCR product and gene counts as a match.

4) Where the PCR product matches in the gene is taken into account.

4) Repetitive sequence filtering is not done.

5) Some genes amplify multiple pcr products. Additional PCR products are included up to 1.5 times the size of the smallest predicted product.