Biomedical Engineering Reference
In-Depth Information
Fig.
7
An example of results for polymerase extension PCR for fragment assembly
a hash index of 7- to 12-mers (allowing up to one mismatch) and
by calculating the local similarity for the whole primer. The
parameters can be altered to allow different degrees of mismatches
at the 3′ end of the primers. The parameters for quick alignment
may be set: the minimum is 0-5 mismatches (default 2 mismatches)
at 3′ end of primer. The program can also handle degenerate
primers or probes, including those with 5′ or 3′ tail sequences. It
includes the detection of non-Watson-Crick base-pairing in in
silico PCR, e.g., the stable guanine mismatches G·G, G·T, and
G·A. Probable PCR products can be found for both linear and
circular templates in both standard and inverse PCR, as well as in
multiplex PCR and using bisulphite-treated DNA. This in silico
tool is useful for quickly analyzing primers or probes against target
