Less tedious procedure for aligning nt sequences

Bill_A_Nussbaumer at ms.bd.com Bill_A_Nussbaumer at ms.bd.com
Mon Jan 11 13:40:12 EST 1999






Bill A Nussbaumer at BDX
01/11/99 01:32 PM

That's a good point, thanks.  My primary computer is a PC so windows
compatible software is my preference.  However, I have access to several
Macs in the lab so I wont rule out helpful suggestions not available on
Wintel machines.  If any Unix software is required the only way I could use
it would be to download bash (or something similar).

Bill Nussbaumer






todd at andrew2.stanford.edu on 01/11/99 12:44:51 PM

To:   Bill A Nussbaumer/BALT/BDX
cc:
Subject:  Re: Less tedious procedure for aligning nt sequences




In article <852566F6.004C4F76.00 at 7crmta_md.ms.bd.com>,
Bill_A_Nussbaumer at ms.bd.com wrote:
>Does anyone have any
>suggestions on how to more quickly get sequences into alignment either
>using DNAStar or otherwise.  I am fairly new to this aspect of DNA
analysis
>and am not completely familiar with all of the Blast and Entrez tools as
of
>yet.
>
You don't say what kind of computer you're using, and since DNAStar is
available for both Windows and Macs, you may get a bunch of irrelevent
responses. But probably the easiest way to do what you want is to get the
freely available ClustalW or ClustalX, which is available for both Macs
and PCs. This program does multiple alignments and provides consensus
sequences and exports a number of different file formats that can be used
by other programs. It reads FASTA format files, which I believe is an
option that Entrez gives you.
You can get ClustalX from:   ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/
There's a bit of a description at:
http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html
Good luck, Todd
--
Dr. Todd Richmond
Carnegie Institution of Washington
260 Panama Street                   Email: todd at andrew.stanford.edu
Stanford, CA 94305                 Homepage: http://cellwall.stanford.edu









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