10/02/14 - Meli'sa Crawford
- New approach for analyzing sequences
New approach for Analyzing DNA sequences
- Instead of using the conventional approach for analyzing DNA sequences through ApE, we aligned our plasmids in Benchiling and searched for missing construct parts. We have an idea of the parts that should be in each plasmid:
BD002: same as BD001 but inserted into vector V0200.
Plasmids BD003-BD006 were checked through Benchiling. The results are the following:
| DNA || Missing Parts ||
| BD003 || 5xGal4 ||
| BD003-2 || PolyA||
| BD004 || HPK ||
| BD004-2 || PolyA ||
|BD005 || N/A ||
|BD005-2 || PolyA ||
|BD006 || 5xGal4, Spacer, CMV, Kozak, AmCyan ||
|BD006-2 || PolyA ||
- BD006- It seems to have D11.12 region only. 5xGal4, Spacer, CMV, Kozak and AmCyan seem to be missing.
- Will verify results with Dr. Haynes.
October 4, 2014:
- PolyA2 is the actual polyA used in the constructs. Realigned the sequences today in Benchiling with RFC23 prefix for the forward sequences and the new polyA and RFC23 suffix for the reverse sequences.
- DPRE may be longer than 800bp, therefore we will not conclude that BD006 does not have any other parts.