software to find restriction site and TM for primer - (Mar/02/2005 )

hi dear all,
I am new in this field. so lots things confused
I have a plasmid from a friend, and get it sequenced. I want to know the restriction site on it, anyone know any software or website can search the restriction site?

another one, I had known a website to calculate the Tm of primer, i can not find it now. does anyone know quite good website for it?

Thanks

hi
for restriction site, as you have the sequence of the plasmid, you can use the free program pDRAW32 available at :

http://medlem.spray.se/acaclone/

here is a ver simple website for tm calculation :
http://www.in-silico.com/tm.php


Fred

For restriction sites, there are a number of online programs such as: TACG, and NEBCutter (in the NEB website).

for primers, there's PRIMER3 or you can go to IDTDNA's website where they have some useful tools.

hi,

Take a look at www.infobiogen/deambulum..... You should get some informations.

good luck,

To get restriction, there are many option. I personaly like the one at http://insilico.ehu.es/restriction (a total of 6 tools related to restriction digest). They have create a open source copy and paste version of one of the tools, and it is available throught BioPHP at http://www.biophp.org/minitools/restriction_digest/demo.php.

For Tm, try http://www.biophp.org/minitools/melting_temperature/demo.php (also open source). It is very simple.

And yet again I will suggest EMBOSS.

www.emboss.org

Enjoy.

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