G***G
发帖数: 16778 | 1 how to design a primer which can distinguish one species from other species?
what kind of technology is it? | f*******o
发帖数: 1 | 2 I would try primer blast from NCBI. It's basically using PRIMER3 to design
primer followed by blast alignment to evaluate specificity.
Paste the sequence of the species-of-interest in the PCR template. In the "
Primer Pair Specificity Checking Parameters" section below, specify the
species you want to avoid the primer to amplify. In this way, the algorithm
will avoid primers having potentials on that species. | G***G
发帖数: 16778 | 3 thank you. I tried the primer blast.
but I couldn't find the parameter to avoid the primer to bind with other
species.
What is the name of the parameter you mentioned to avoid the primer to
amplify?
algorithm
【在 f*******o 的大作中提到】
: I would try primer blast from NCBI. It's basically using PRIMER3 to design
: primer followed by blast alignment to evaluate specificity.
: Paste the sequence of the species-of-interest in the PCR template. In the "
: Primer Pair Specificity Checking Parameters" section below, specify the
: species you want to avoid the primer to amplify. In this way, the algorithm
: will avoid primers having potentials on that species.
| f*******o
发帖数: 1 | 4 Just putting a value in the "Organism" field of the "Primer Pair Specificity
Checking Parameters" section is enough. Click the question marker followed
by each parameters to learn more, such as
"With this option on, the program will search the primers against the
selected database and determine whether a primer pair can generate a PCR
product on any targets in the database based on their matches to the targets
and their orientations. The program will return, if possible, only primer
pairs that do not generate a valid PCR product on unintended sequences and
are therefore specific to the intended template. Note that the specificity
is checked not only for the forward-reverse primer pair, but also for
forward-forward as well as reverse-reverse primer pairs." | k***b
发帖数: 181 | | k***b
发帖数: 181 | | G***G
发帖数: 16778 | 7 I set organism as Ixodes and got the following output. Does it mean
the designed primer bind well with the target organism (Ixodes) or not?
What I want is a primer which doesn't bind with the target organism (Ixodes).
Thanks.
Products on target templates
>XM_002400420.1 Ixodes scapularis map-kinase activating death domain protein
, putative, mRNA
product length = 3845
Forward primer 1 CAGCAGCCGCGGTAATTCC 19
Template 88 GT........C.G..C... 106
Reverse primer 1 CCCGTGTTGAGTCAAATTAAGC 22
Template 3932 ...CA......CA.......A. 3911
Specificity
followed
targets
【在 f*******o 的大作中提到】
: Just putting a value in the "Organism" field of the "Primer Pair Specificity
: Checking Parameters" section is enough. Click the question marker followed
: by each parameters to learn more, such as
: "With this option on, the program will search the primers against the
: selected database and determine whether a primer pair can generate a PCR
: product on any targets in the database based on their matches to the targets
: and their orientations. The program will return, if possible, only primer
: pairs that do not generate a valid PCR product on unintended sequences and
: are therefore specific to the intended template. Note that the specificity
: is checked not only for the forward-reverse primer pair, but also for
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