[BioPython] AlignIO: Sequences of different length

João Rodrigues anaryin at gmail.com
Fri Dec 5 06:34:33 EST 2008

I got a reply from the EBI support team saying that the webserver they
provide is outdated, when compared to the versions of NEEDLE we (me on the
web and Peter on his local machine) used. So, BioPython is nice and
up-to-date, it's their server that is quite outdated.

" Actually the WSEmboss web service uses an older version of EMBOSS (2.9.0),
exibits this behaviour. I suggest you contact the BioPython folks and let
know that older versions of EMBOSS behave differently.

If you want to use the latest version of EMBOSS I suggest looking at using
Soaplab services (see

All the best,

Support at EBI"

João Rodrigues

On Thu, Dec 4, 2008 at 7:57 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Thu, Dec 4, 2008 at 6:19 PM, João Rodrigues <anaryin at gmail.com> wrote:
> > I believe the script I gave you had the needle function on it :x It's
> just a
> > simple WSDL file provided by EBI being used by the SOAPpy module to
> access
> > the webservice. The parameters are default as well so, gapopen 10.0 and
> > gapextend 0.5.
> Oh yes - I see it now on pastebin, previously I'd only looked at the
> output file.
> > The page of the service is:
> > http://www.ebi.ac.uk/Tools/webservices/services/emboss
> >
> > I kind of noticed that non-sense gap, but that comes with the format
> > unfortunately. I ran the Web version of the program, not the webservice,
> and
> > the outcome was the same (regarding the gap):
> >
> >
> http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/needle/needle-20081204-18180513899973.html
> >
> So the web versions of EMBOSS are using spaces for leading gaps
> (program version unknown), while the standalone version of EMBOSS (up
> to version 6.0.1) are using dashes (minus signs).  Biopython 1.49
> expects the leading dashes.
> I suspect that the EBI are running a more recent not-yet-released
> version of the EMBOSS tools to power their webservices.  I'm not
> familiar enough with their code to know where to look...
> I suggest you email the webservice people and ask them why the needle
> output is different to the command line version (tell them parsers
> such as Biopython may be broken by this change).
> If this is a forthcoming change to the EMBOSS standalone tools, then I
> guess we'll have to fix the parser anyway.  I may find time to look at
> this over the weekend - we'll see.
> Regards,
> Peter

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