summary of *oligo construction programs*

Mario Nenno [Biologie] nenno at rhrk.uni-kl.de
Wed May 29 13:20:17 EST 1991


Hello netlanders,

Summary of my *WANTED: OLIGO construction program* question:
------------------------------------------------------------

<>today I search a program which help us to construct an oligo as
<>good as possible. 
<>
<>We think because so many people had to to this so many times, and
<>the needs are always the same ( providing not complementary primers
<>against each other, enough length for identification ...) it might
<>be possible that someone has already written a little programm which
<>does this task.
<>
<>We would greatly apreciate any PD/freeware/shaware as source files
<>(Pascal or C) or binary for DOS or UNIX machines (DOS prefered).

>>>>>>>>>>>>>>>>>>>>> Summary from responses: <<<<<<<<<<<<<<<<<<

Nuc-it
        CompuRight, (301) 963-9460
        $199

        30-day trial version available

OLIGO (later renamed NAR) by Wojciech Rychlik
        See Nucl. Acids Res. 17:8543-8551 for his address.
        He'll send it to you for free if you provide disc and 
        self-addressed stamped mailer.  

        A greatly expanded version, now called OLIGO is commercially
        available from National Biosciences (see below)

OLIGO (see above, by Wojciech Rychlik)
        National Biosciences, 725, Tower Dr., Hamel, MN  55340.  
        about $600 US

        optimal primer pairs for PCR,find oligos that don't form
        hairpins, optimal hybridization temperatures, optimal annealing
        conditions for PCR, correct for salt/formamide concentrations,
        find false priming sites and palindrome sequences,calculate
        all thermodynamic parameters for duplexes, works with
        ambigous base symbols for DNA and RNA, compatible with most
        sequence file formats. Mac version to appear late in 1990.

Primer, by Gene Shpaer, gene at jmullins.Stanford.EDU
        anonymous ftp to jmullins.stanford.edu (36.45.0.126)
        cd pub

        *program on Sun ("C") that finds potential mispriming sites for 
        already designed primers.  This program is important when you
        amplify *big* DNA fragments and mispriming whin the amplified
        region would lead to amplification of the shorter fragment.*


Primers (Nuc. Acids Res. (1990) 18(7):1757-1761),
        The Henry M Jackson Foundation, 1426 Rockville Pike, Suite 400
        Rockville, Maryland USA 20852, Attn: PCR - Betty McAuliffe
        $50 US

        It will scan a sequence and select suitable primers based on 
        parameters of length, G+C content, and melting temperature,
        as set by the user. It will also check for the ability to 
        form hairpins. 

Primer Detective
        Nucleic. Acids Res 18(7)1757(1990)
        For a free demo disk call (800) 662-CLON Its from CLONTECH


>>>>>>>>>>>>>>>>>>>>> Here are the responses <<<<<<<<<<<<<<<<<<<<<<

FROM: Walter Hill
BITNET: WEH at FDACFSAN.bitnet
 
>There are a number of programs that have been developed:
>1. Primer Detective: For a free demo disk call (800) 662-CLON Its from CLONTECH
>   see Nucleic. Acids Res 18(7)1757(1990)
>2. Nuc-it: $199 from CompuRight, (301) 963-9460
>   30-day trial version available
>3. OLIGO (later renamed NAR) by Wojciech Rychlik. See Nucl. Acids Res.
>   17:8543-8551 for his address.  He'll send it to you for free if you provide
>   disc and self-addressed stamped mailer.  A greatly expanded version, now
>   called OLIGO is commercially available from National Biosciences, 725
>   Tower Dr., Hamel, MN  55340.  Unfortunately, it costs about US$600.
> 
>It would be appreciated if you could post a summary of the responses you
>receive on the network.



FROM: Peter Markiewicz
INTERNET: JMILLER%VXBIO.SPAN at STAR.STANFORD.EDU:
 
(from his: Public Domain/Commercial Program List For Molecular
           Biology using the Apple Macintosh (April 1990 version) )

>Oligonucleotide/PCR Design:
> 
>OLIGO National Biosciences, 725 Tower Drive, Hamel, MN 55340
>612-478-6626 FAX:612-478-2375
>Commercial program for analysis of primer sequences. Capable
>of the following analyses:
>optimal primer pairs for PCR,find oligos that don't form
>hairpins,optimal hybridization temperatures, optimal annealing
>conditions for PCR,correct for salt/formamide concentrations,
>find false priming sites and palindrome sequences,calculate
>all thermodynamic parameters for duplexes,works with
>ambigous base symbols for DNA and RNA,compatible with most
>sequence file formats. Mac version to appear late in 1990.



FROM: Gene Shpaer
INTERNET: <gene at jmullins.Stanford.EDU>

>I have a program on Sun ("C") that finds potential mispriming sites for already
>designed primers.  This program is important when you amplify *big* DNA
>fragments and mispriming whin the amplified region would lead to amplification
>of the shorter fragment.
>
>You can get the program by anonymoud ftp to jmullins.stanford.edu
>(36.45.0.126),
> cd pub



FROM: Pearse Ward
INTERNET: misra at herald.usask.ca (?)

>I don't know of any freeware just yet (I'm working on one), but we have 
>received a quite good program from the Henry M Jackson Foundation. It is 
>called "Primers" (Nuc. Acids Res. (1990) 18(7):1757-1761), and is available 
>for the low price of $50 US. It will scan a sequence and select suitable 
>primers based on parameters of length, G+C content, and melting temperature, 
>as set by the user. It will also check for the ability to form hairpins. I 
>think that it is well worth the cost. The address to write to is:
>
>The Henry M Jackson Foundation
>1426 Rockville Pike, Suite 400
>Rockville, Maryland USA 20852
>Attn: PCR - Betty McAuliffe



I want to thank Walter Hill, Peter Markiewicz, Gene Shpaer and
Pearse Ward who replied to my question and hope that this short
list may help others too.

P.S.
I hope its OK to use personal responses in a summary in this
form. Any flames (if any), directly to my adress below).

!! DISCLAIMER:
!! I list these descriptions from resoponses to my question in a
!! newsgroup. I  d o n ' t have any connections to any author
!! or company. Nor can I provide any program.
!!
!! For any questions please mail only to those I got the mail from.
!! The e-mail adresses are on top of every item.



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