Less tedious procedure for aligning nt sequences

Manfred Friedrich mfriedr2 at gw.ford.com
Sun Jan 17 07:08:58 EST 1999


Bill_A_Nussbaumer at ms.bd.com wrote:
> 
> 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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