Methods Digest, Vol 44, Issue 12

Virash Gupta via methods%40net.bio.net (by virashkgupta from gmail.com)
Sat Jan 17 00:19:58 EST 2009


FastPCR from primer digital ltd is freeware and complete solution for primer
designing with excellent additional features.

To academic institutions FastPCR is available for a free, provided for
non-commercial research and education use only (not for reproduction or
distribution, cannot be used in any commercial enterprises).

The manual, licence and files for installation are available over the
Internet at:

http://www.biocenter.helsinki.fi/bi/programs/fastpcr.htm

or from PrimerDigital Ltd: http://www.primerdigital.com/

all the best
On 1/14/09, methods-request from oat.bio.indiana.edu <
methods-request from oat.bio.indiana.edu> wrote:
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> Today's Topics:
>
>   1. Re: DNA software question (Nick Theodorakis)
>   2. RE: DNA software question (Zhonglin Chai)
>   3. Re: DNA software question (chovek69)
>   4. Re: DNA software question (Aawara Chowdhury)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 12 Jan 2009 19:04:12 -0800 (PST)
> From: Nick Theodorakis <nick.theodorakis from gmail.com>
> Subject: Re: DNA software question
> To: methods from net.bio.net
> Message-ID:
>        <b9d01866-dc25-4ea9-a6db-9469b440ca79 from f40g2000pri.googlegroups.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
>
>
> Han wrote:
> > Colleague at Cornell Medical College has a very old Mac with an old
> version
> > of DNAStar, which he likes very much.  His use is not very intensive, but
> > primer design, sequence alignment etc are used relatively often.
> >
> > Since the Mac is about to die, he would like software for a PC (XP Pro)
> > that could best perform those functions.  DNAStar (new version) costs
> > $1,000/year in licensing costs, which colleague doesn't regard as a wise
> > investment.  What are his best options for free or cheap software with
> > similar capabilities as what he wants of DNAStar (primer design, sequence
> > alignment, etc)?
> >
>
> For primer design, I and nearly everyone I know use Pimer3. There is a
> web version:
>
> <http://frodo.wi.mit.edu/primer3/input.htm>
>
> which is also now built into the NCBI primer blast page:
>
> <http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?
> LINK_LOC=BlastHome>
>
> Downloadable source is also available:
>
> <http://primer3.sourceforge.net/>
>
>
> --
> Nick Theodorakis
> nick_theodorakis from hotmail.com
> contact form:
> http://theodorakis.net/contact.html
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 13 Jan 2009 14:16:42 +1100
> From: "Zhonglin Chai" <Zhonglin.Chai from bakeridi.edu.au>
> Subject: RE: DNA software question
> To: "Han" <nobody from nospam.not>, <methods from magpie.bio.indiana.edu>
> Message-ID:
>        <217613C88C00D4448B099AD7A374F25302C971D0 from exch01.bhri.internal>
> Content-Type: text/plain;       charset="us-ascii"
>
> Try online softwares. You can start from this link:
> http://www.expasy.ch/tools/
>
> Dr Zhonglin Chai, PhD
>
> -----Original Message-----
> From: methods-bounces from oat.bio.indiana.edu
> [mailto:methods-bounces from oat.bio.indiana.edu] On Behalf Of Han
> Sent: Tuesday, 13 January 2009 01:14 PM
> To: methods from magpie.bio.indiana.edu
> Subject: DNA software question
>
> Colleague at Cornell Medical College has a very old Mac with an old
> version of DNAStar, which he likes very much.  His use is not very
> intensive, but primer design, sequence alignment etc are used relatively
> often.
>
> Since the Mac is about to die, he would like software for a PC (XP Pro)
> that could best perform those functions.  DNAStar (new version) costs
> $1,000/year in licensing costs, which colleague doesn't regard as a wise
> investment.  What are his best options for free or cheap software with
> similar capabilities as what he wants of DNAStar (primer design,
> sequence alignment, etc)?
>
> --
> Best regards
> Han
> email address is invalid
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>
> ------------------------------
>
> Message: 3
> Date: Tue, 13 Jan 2009 00:33:09 -0800 (PST)
> From: chovek69 <ivanoov from gmail.com>
> Subject: Re: DNA software question
> To: methods from net.bio.net
> Message-ID:
>        <43566c93-a960-4f46-97d5-5a265496504a from q35g2000vbi.googlegroups.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Jan 13, 5:04 am, Nick Theodorakis <nick.theodora... from gmail.com>
> wrote:
> > Han wrote:
> > > Colleague at Cornell Medical College has a very old Mac with an old
> version
> > > of DNAStar, which he likes very much.  His use is not very intensive,
> but
> > > primer design, sequence alignment etc are used relatively often.
> >
> > > Since the Mac is about to die, he would like software for a PC (XP Pro)
> > > that could best perform those functions.  DNAStar (new version) costs
> > > $1,000/year in licensing costs, which colleague doesn't regard as a
> wise
> > > investment.  What are his best options for free or cheap software with
> > > similar capabilities as what he wants of DNAStar (primer design,
> sequence
> > > alignment, etc)?
> >
> > For primer design, I and nearly everyone I know use Pimer3. There is a
> > web version:
> >
> > <http://frodo.wi.mit.edu/primer3/input.htm>
> >
> > which is also now built into the NCBI primer blast page:
> >
> > <http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?
> > LINK_LOC=BlastHome>
> >
> > Downloadable source is also available:
> >
> > <http://primer3.sourceforge.net/>
> >
> > --
> > Nick Theodorakis
> > nick_theodora... from hotmail.com
> > contact form:http://theodorakis.net/contact.html
>
> and for seq alignment Bioedit and MEGA 4...
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 13 Jan 2009 14:33:13 GMT
> From: Aawara Chowdhury <aawara from pontiff-playground.org>
> Subject: Re: DNA software question
> To: methods from net.bio.net
> Message-ID: <JC1bl.30686$JA5.24134 from newsfe08.iad>
> Content-Type: text/plain; charset=us-ascii
>
> In <Xns9B91D7F826D69ikkezelf from 216.151.153.22>,
> Han <nobody from nospam.not> wrote:
>
> > Since the Mac is about to die, he would like software for a PC (XP Pro)
> > that could best perform those functions.  DNAStar (new version) costs
> > $1,000/year in licensing costs, which colleague doesn't regard as a wise
> > investment.  What are his best options for free or cheap software with
> > similar capabilities as what he wants of DNAStar (primer design, sequence
> > alignment, etc)?
> >
>
> We use "ApE" (A Plasmid Editor) and "Serial Cloner".
>
> ApE is available from:
> <http://www.biology.utah.edu/jorgensen/wayned/ape/>
>
> Serial Cloner is available from:
> <http://serialbasics.free.fr/Serial_Cloner.html>
>
> Both are free, although a donation is suggested for Serial Cloner.
>
> ApE reads ABI sequencing trace files, does restriction digests,
> sequence alignments, finds primers, finds silent restriction endonuclease
> recognition sites, does translations, produces excellent annotated
> plasmid maps, and can BLAST sequences.
>
> Serial Cloner does everything that ApE does, and in addition, shRNA
> design, Gateway(tm) cloning design, and one can setup ligations of
> 1, 2, or 3 fragments.  The plasmid maps generated by Serial Cloner are
> similar to those made by DNA Strider (i.e. restriction sites but not
> annotated).
>
> AC
> --
> Email: echo 36434455860060025978157675027927670979097959886449930P | dc
>
>
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> End of Methods Digest, Vol 44, Issue 12
> ***************************************
>



-- 
Dr V K Gupta
Sr Microbiologist (Molecular Biology)
Insect Molecular Biology Lab
Department of Entomology
Punjab Agricultural University
Ludhiana (Pb)-141004- India
M: 09815963210


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