Less tedious procedure for aligning nt sequences

Bill_A_Nussbaumer at ms.bd.com Bill_A_Nussbaumer at ms.bd.com
Mon Jan 11 09:10:09 EST 1999






Bill A Nussbaumer at BDX
01/11/99 09:02 AM

Hi all,

I'm in the process of a 10 day evaluation of the Lasergene DNA analysis
software package.  I'm currently trying to use megalign to determine
consensus between a gene among numerous organism strains.  Performing an
Entrez search yielded 27 different sequences of interest.  I exported these
sequences into a single text file and then cut and paste them into their
own individual text files.  Following this I used the EditSeq module of the
software to convert the sequence files into *.seq files one at a time.  At
this point it was easy to enter the files into Meg-align but the first
steps of this procedure are quite tedious.  With only 27 sequences it's
bearable (it took about 30 - 45 minutes), but in the future if I have
hundreds of genes this method would be unacceptable.  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.

Thanks for any suggestions,

Bill Nussbaumer






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