[Bioperl-l] Generate a hsp from emboss format?

[Peter Cock]

On Mon, Mar 18, 2013 at 11:43 AM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>
> Hi,
> I have a script who uses emboss (water) for a dynamic programming alignment.
> Is this possible to generate (convert) my result in emboss format in a hsp
> (blast) like.
>
> I need (I think) an hsp format because it's much easier for parse only one
> of the two strand in the alignment (and this is what I need).
>
> Thanks!

EMBOSS water (and related tools like needle) support a range of output
formats - have you looked at those yet?

Peter