|
Phage sequences in bacterial genomes
The truth behind Blast
Alignment of P2 genes to find primers
|
To find the primers to be used in the screening, you focus on a protein you believe to be highly conserved amongst P2-like phage, the P gene, encoding a protein involved in the packaging of the phage head. You collect and align P gene sequences from as many P2-like phage sequences you can find. A small portion of the alignment is shown to the right.
|
P2
GNNGAKLIFLGTNSNT
L413
GNNGAKLIFLGTNSNT
186
GNNGAKLIFLGTNSNT
CTX
P-NGAELHFLGTNART
K139
S-NGAELHYLSTNGKT
HP2
S-NGAELHFLSTNKNT
Region of P gene from P2-like phage
|
Looking at the aligned sequences, you see that it might be difficult finding a region common to all P2-like phage. For the moment, you choose to focus on the phages most closely related to P2 and design a primer that matches the DNA encoding the
NGAKLIFL region and a second primer from another conserved region. You can get the primers here.
These primers should recognize P2 and its close relatives. But are they specific enough not to also recognize host DNA?
Back to main Scenario page back one page continue
|
