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Introduction
Primer Validator is a scientific utility which allows researchers
to verify whether the designed primer is unique for the gene
of interest or not. It will be useful if that gene is a member
of a large superfamily. In addition, researchers may want to
check if the oligonucleotide at the 3´ end can bind to
the cDNAs of other genes within the same superfamily. Because
most primer-designing programs do not automatically search
for matched sequences in other genes, Primer Validator will
help researchers to search inside multiple genes simultaneously,
and select the best designed primer which is specific to the
studied gene.
Please note that the Primer Validator is not a primer-designing
program. You must have a list of primers for the studied
gene first. Please also read the Instruction inside
the downloaded package for more informations.
Features
1. Enter the
upper primer here.
2. Enter the lower primer here.
3. Sequence list
- You can save this
list by using the Save List command of the File menu.
- To open the saved
list,
just double-click
on the file icon on your desktop, or drop the saved file on this
area.
- You can also double-click
on the list to open the target sequence.
- To delete a file
from the list, please use the Delete key from your keyboard.
- The
numbers on the second and third column of the list represent
matched upper and lower primers, respectively.
- To sort the list, use the Sort List command of the Edit menu.
4. Displaying canvas. You can open the sequence files by dropping
the files on this area.
5. Search button: press this button to begin searching all listed
files.
6. Current search area: this area will show you the currently active
primers.
7. Position
of upper and lower primers:
- Optional.
- If you enter
numbers here, the engine will underline found sequences
within those positions, and label them with red
and blue color, respectively, otherwise
the engine will label them with orange and magenta.
- If the sequence file contains matched oligonucleotides, the yellow
icon on the file list will be changed to be a
magenta icon.
 
 
8. Summary of the search engine.
9. Name
of the active file.
Sequence
Files
The sequence file can be obtained from an online database, e.g. http://www.ncbi.nlm.nih.gov/.
It is in FASTA format and has ".txt" extension (can be created
by Apple's TextEdit). Please see the example below. Primer Validator will
not read the information beginning
with " > " sign, therefore, you can add any information inside
the sequence file - just make sure that you have " > " in
front of that information. The first line with " > " should
be the gene's name, so it will be read by the engine and show on the "Gene" area
of the main window.
Requirement
- Mac OS X
10.2 or later
- QuickTime
5.0 or later
Language
support
If
you want to translate Primer Validator, please contact me
at: naratt@naratt.com
Registration Primer Validator
is a shareware.
- Single user
license US$ 15.00
- Site license
US$ 120.00
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English
: by Narattaphol Charoenphandhu (
