[EMBOSS] GCG: FRAMEALIGN- align protein-6 frames of DNA

[Jason Stajich]

What is wrong with using tfasty/tfastx (FASTA package)?

fastx3/ fasty3 Compare a DNA sequence to a protein sequence database,
               by comparing the translated DNA sequence in three
               frames and allowing gaps and frameshifts.  fastx3 uses
               a simpler, faster algorithm for alignments that allows
               frameshifts only between codons; fasty3 is slower but
               produces better align- ments with poor quality
               sequences because frameshifts are allowed within
               codons.

tfastx3/ tfasty3 Compare a protein sequence to a DNA sequence
                 database, calculating similarities with frameshifts
                 to the forward and reverse orientations.

tfasta3 Compare a protein sequence to a DNA sequence database,
	calculating similarities (without frameshifts) to the 3
	forward and three reverse reading frames.  tfastx3 and tfasty3
	are preferred because they calculate similarity over
	frameshifts.


-jason
On Fri, 26 Sep 2003, Lakshmanan Iyer wrote:

> Hello,
>
> Is there an EMBOSS equivalent of GCG:FrameAlign?
>
> It creates an optimal alignment of the best segment of similarity (local
> alignment) between a protein sequence and the codons in all possible reading
> frames on a single strand of a nucleotide sequence. Optimal alignments may
> include reading frame shifts.
>
> This is a very crucial tool for the evolutionary biologists.
>
> -thanks
>
> -laxman
>
>
>
>
>
> Lakshmanan Iyer, Ph. D.
>
> Computational Biologist
>
> Manager of Collaboration and Training
>
> Computational Biology Group
>
> Bauer Center for Genomics Research
>
> Bauer Laboratory
>
> 7 Divinity Ave.
>
> Cambridge, MA 02138
>
> www.cgr.harvard.edu <http://www.cgr.harvard.edu>
>
> Phone:617-384-7647
>
> Fax: 617-495-2196
>
>
>
>

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