[BiO BB] Re: BIO_Bulletin_Board digest, Vol 1 #10 - 2 msgs

[kiran challapalli]

Hi all,

Can anybody tell me wether there are any
Bioinformatics programs (online and downloadable)
which are compatable for running parallely on linux
cluster. For example are there any parallel clustalw
or parallel blast available?
If available, please mention the site address.
with regards,

Kiran Kumar.c
Scientist,
DSQ Biotech,
India




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> Today's Topics:
> 
>   1. Re: primer pairings (Bela Tiwari)
>   2. Re: Linux Clustering for Bioinformatics???
> (Felipe G. Nievinski)
> 
> --__--__--
> 
> Message: 1
> Date: Tue, 13 Mar 2001 15:56:43 +0000 (GMT)
> From: Bela Tiwari <btiwari at molbiol.ox.ac.uk>
> To: huseyin uysal <uysal at doctor.com>
> cc: bio_bulletin_board at bioinformatics.org
> Subject: Re: [BiO BB] primer pairings
> 
> >I need a free software or internet site for
> designing primers.
> >especially, I need a program that shows potential
> pairings of a primer in
> >the given sequence. I mean, I paste the sequence
> into the program window and
> >also I paste the primer then this program
> calculates and shows potential
> >pairings  on the pasted sequence and on its
> complementary sequence. Thank
> >you very much...
> 
> My favorite program for this (when I used to do it!)
> was a Mac program
> called Amplify. Its available, I believe, from:
> 
> http://www.wisc.edu/genetics/CATG/amplify/ 
> 
> If you don't have access to a Mac, there is an
> applet at 
> 
>
http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html
> 
> which will test two primers against themselves and
> each other for
> hairpins, repeats, dimer formation, etc, etc.
> However, I don't think you
> can check for where along a sequence your primers
> might bind  using this
> site. (If you do use a Mac, you probably won't be
> able to use this site
> unfortunately.)
> 
> 
> Other than that I'll just give you a couple of sites
> that list various
> primer programs that are out there (which I
> personally find useful
> references)
> 
> 1) The primer list at the HGMP:
> 
> http://www.hgmp.mrc.ac.uk/GenomeWeb/nuc-primer.html
> 
> 
> 2) There are reviews of various primer packages,
> (some free and some not)
> here:
> 
> http://www.bbsrc.ac.uk/molbiol/reviews.html
> 
> 
> good luck. 
> 
> 
> Bela
> 
> 
>
.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> Dr. Bela Tiwari                Bioinformatics
> Officer
> OU Bioinformatics Centre          
> South Parks Road,                  01865 (2)75507 
> Oxford  OX1 3RE              
> http://www.molbiol.ox.ac.uk
>
.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> 
> 
> 
> --__--__--
> 
> Message: 2
> From: "Felipe G. Nievinski" <fnievinski at cpovo.net>
> To: <bio_bulletin_board at bioinformatics.org>
> Subject: Re: [BiO BB] Linux Clustering for
> Bioinformatics???
> Date: Tue, 13 Mar 2001 15:47:36 -0300
> charset="Windows-1252"
> 
> Hi.
> 
> It worth to keep an eye on the NCSA website, about
> applications.
> http://www.ncsa.uiuc.edu/
> 
> For example, the last published 'Cover Story' was:
>
http://www.ncsa.uiuc.edu/access/CoverStories/phylogeny/
> Gene data allow researchers to recover the
> evolutionary history of plants,
> but even the smallest dataset can require impossibly
> large computations.
> Using an Alliance Linux cluster and newly designed
> software, a team from the
> University of New Mexico and the University of Texas
> have increased the
> speed of the process millionfold for one family of
> plants.
> 
> 
> Best regards,
> Felipe Nievinski.
> 
> 
> 
> 
> --__--__--
> 
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> End of BIO_Bulletin_Board Digest


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