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using primers programms - (Jun/15/2007 )

hi every body
can someone please suggest a good primer site that can be easy to use as i entered on pe site but it doesnt give me any results
u see i have primerrs ( 3 sets for 3 areas n the Y chromosome ) i need to know what band size to expect
thanks alot

-lula-

To find out the expected band sites you should BLASTn search your primers. You can calculate your amplicon sizes from the alignment to the gDNA or cDNA respectively.

-kr├╝melmonster-

If you need to design a new pair of primers, I will suggest you to use primer3.
It's reliable and user friendly but has a lot of selectable options...

-ila-

Primer3
is easy to use and the best is FREE!!!! and give several options.

-merlav-

i used the P3 before but the window doesnt work
???? i put the primwr on left side and the reverse on the other sside and click but nothing happens !!!!!!

-lula-

Lula, if you already have the primer sequence, Primer3 won't help you. You need to align the primers to the gDNA or cDNA (whatever you are looking at) and this is most convenient done by BLASTn. All Primer software is there to pick primers from a given sequence. As you already have three different primer pairs, these programs are pretty much useless for you...
BLASTn can be found at Entrez Nucleotide ... here!

-kr├╝melmonster-

i will try it
thanks hope it works

-lula-

There is a site, that does Virtual PCR.
Sometimes it doesn't show any results, even if PCR gives nice product, but sometimes it works OK.
I would try it first, it it founds nothing, then only Blast, calculator and some time.

BTW I use Primer3 to check primers I find elsewhere, you just need to feed it with a big sequence of the region you know primers are in, but not sure where exactly.

-Trof-

yeh, primer 3 is good.

-scolix-

and where to get the sequence from ???

-lula-