ISHH Probe Design - (Jul/31/2007 )

How hard can it be to find an online program which can design oligos for use in ISHH according to given specifications?
Apparently, damn hard.
I'm either bringing up Oligo Calcs (excellent ex-post anyway) or PCR primer progs that max out at 36mers on every other search.

Q:
Does anyone know of any online progs for designing ISHH probes? (requisite specs below)

Thanks in advance!

Cam

FYI, my oligo design specs are from Erdtmann-Vourliotis et al 1999 (Brain Res Prot (4), 82-91):
>Melting temperature 100-106C
>GC content 48-62%
>Length 42-54 nucleotides
>Hairpins 0-neg4.7 kcal
>Length of runs up to five

<EDIT>
All good. Doing FASTA line-by-line analysis using the Sigma-Aldrich DNA Calc and OligoCalc on decent probes.
If I have to do a stack of these again I may have to write something, because this is abysmal.
Word.
</EDIT>

-rH_-

Never mind peeps (not that you did anyway),
I'm going to write my own.

c.

QUOTE (rH_ @ Jul 31 2007, 07:05 PM)

FYI, my oligo design specs are from Erdtmann-Vourliotis et al 1999 (Brain Res Prot (4), 82-91):
>Melting temperature 100-106C
>GC content 48-62%
>Length 42-54 nucleotides
>Hairpins 0-neg4.7 kcal
>Length of runs up to five

<EDIT>
All good. Doing FASTA line-by-line analysis using the Sigma-Aldrich DNA Calc and OligoCalc on decent probes.
If I have to do a stack of these again I may have to write something, because this is abysmal.
Word.
</EDIT>

-rH_-

OK, so I got round to coding it. Used mod_python for Apache. Check it out at:
http://128.250.222.24/pPG/

If you have any development suggestions, particularly with respect to code for secondary structure or primer dimer formation, let me know.

Cheers,
Cam.

-rH_-