[Bioperl-l] HELP!!! ALIGN TWO SIMPLE DNA SEQ. USING BIOPERL

[Jason Stajich]

This has been covered on the list and is in the FAQ I believe.
pSW is for protein Smith-Waterman alignments only.

We don't support DNA alignments directly but you can use the EMBOSS
program 'water' to generate a the best local alignment with smith-waterman
or 'needle' to generale a Needleman-Wunsch global alignment.  There is an
interface to EMBOSS programs called Bio::Factory::EMBOSS.  There is an
example of how to use it in the FAQ.  NB this is only for unix installs.

-jason

On Tue, 7 May 2002, Ze Cheng wrote:

> Hello,
>       Could someone please kindly tell me how to align two DNA sequence
> using any possible bioperl software. I have tried clustalw in vain with a
> unresolved segmentation fault (the authors email does not work), pSW which
> only aligns protein, blast that always give me sth like "Unable to get
> Karvin-A. score". Besides, bioperl's doc does not tell you how to turn off
> the filter. I am desperate now. Thank you for any useful information.
>       ginger
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu