*Primer programs

John Nash num208jn at MBDS.NRC.CA
Mon Apr 13 14:20:57 EST 1992


In article <9204102213.AA04100 at welchgate.welch.jhu.edu>, danj at WELCHGATE.WELCH.JHU.EDU (Dan Jacobson) writes:
>
>
>Patrick Twomey writes:
>
>>>I'm looking for a primer analysis software (commercial or share-)
>>>for Mac Intosh;
>>>What could be the best choice
>>>The purpose is to analyse multiple proteines sequences and get the best
>                            ^^^^^^^^^^^^^^^^^^        
>>>pair of primers for PCR

[stuff deleted]

>Hmm, something is missing here.  The original request was for a program
>which looks at multiple PROTEIN sequences and chooses pcr primers.
>I assume that Jean_Marc is looking to pull up new members of a Superfamily,
>say protein kinases, and has an alignment and wants to choose the best
>pcr primers from that.  Now the propaganda from Oligo doesn't say anything
>about looking at protein sequences for primer designation - if it actually
>does this - great!, if not there are at least two programs (one of which I know
>has been compiled on a Mac) which design primers which are FTP`able. 
>Off-hand I can't think of an FTP`able program which looks at protein
>sequence and designs primers.  
>I still have the info from a a few months ago where there was a rather
>lengthy thread on the ftp`able primer programs and will pass it along to
>anyone who is interested.  As usual I'll repost it if the demand becomes large.
>
>Best of luck,
>
>Dan Jacobson
>
>danj at welchgate.welch.jhu.edu
> 

I have written a program for the IBM-PC family which will do much of
what the original poster wants.  Basically, my program will take amino
acid strings up to 70 residues, reverse translate them and generate
oligomers based on:  Max or min length, max desired degeneracies and
(if desired) codon preference bias.  

Good news:	1.  It's absolutely free.   
			2.  It accounts for problems in reverse-translation of Arg, 
Leu and Ser because of their six codons.

Bad news:	1. It will only work on VGA/EGA card-driven monitors, because
I alter the screen fonts and you can't do that with CGA or Hercules.
		2. It's runs under MS-DOS only, and is probably not portable 
to other platforms (If I had decent access to a UNIX box or a Mac with a
compiler, things would be different).
		3. It doesn't align proteins and then look for primers.  I
had considered incorporating this feature, but in practice, I find it
easier to use the alignment programs already written.  I figure that
sequence alignment needs a lot of manual manipulation for the results
to be usable (in my hands and with the data I've looked at).  I prefer
to use something like GCG and MALIGNED to do my protein alignments,
then pull out nice alignments of peptide to feed to my program for it
to spit out potential primers.
		4. You have to supply your owm codon preferences, but the
program has a codon preference editor built in.
		5. It's in "wide beta" i.e. I think I have made it bug free,
and I have sent it to some colleagues who are trying to prove me
wrong.

I have submitted the paper describing it, and I was going to hold off
releasing it until I had heard from the journal, but if there's enough
interest from bionet.software folk, I'll send it to a few fileservers
(sorry I can't email copies to folk, the network folk here go nuts if
I do that).


John Nash     (Internet:) Nash at biologysx.lan.nrc.ca.  
Email to my other addresses is forwarded automatically,
Disclaimer:  All opinions are mine, not NRC's!




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