Tool for searching optimal oligonucleotide, ISH? - (May/17/2005 )
Hi!
I am wondering if anyone knows about a tool for selecting optimal oligonucleotides of length 30-50nt for In Situ Hybridizations. Either by entering a full-length mRNA sequence or by entering the accession number.
Is there any software? Free online tool?
In that tool It would be beneficial to be able to enter GC content and Melting temperature.
Thanks! 
I am wondering if anyone knows about a tool for selecting optimal oligonucleotides of length 30-50nt for In Situ Hybridizations. Either by entering a full-length mRNA sequence or by entering the accession number.
Is there any software? Free online tool?
In that tool It would be beneficial to be able to enter GC content and Melting temperature.
Thanks!
Yeah, I wouldn like to know such a tool
I always pick a sequence and blastn it at ncbi for homologies. If that is fine then I go ahead and order it. Usually the choice is limited anyway (i.e. no repeats or GC rich sequences)
Hi
Quick reply since your Q is similar to one I just answered. We used a company called GeneDetect, www.genedetect.com several years ago to design our probes and it worked well (that is, for our radioactive ISH). At that time, just like you, I couldn't find an all-in-one design tool like the one you are looking for. For $59 they can just design the sequences for you (that was 2002/2003 prices, you'll need to check recent prices) or design and then make the probes for you too.
Don't forget for ISH you want highly purified probes to prevent too much background. HPLC or cartridge-purification works well.
Bye