-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Jayashankar,
sorry, you did explain this in your model and I flipped clustalo with clustalw. Even though when I used the option '-convert', clustalw does not re-align the input but simply converts it, so in case it can read the clustalo output, this should do the job, shouldn't it? Have you tried reading the output file with clustalx or seaview or jalview? These programs should be able convert to various file formats without messing up with the alignment. Cheers, Tim On 03/27/12 15:44, Jayashankar wrote: > Dear Tim, > > I try to model a full length protein based on various domains solved > already. > In that case, alignment of multiple sequence should approximately locate to > the corresponding domain region. > > Clustalw results in an unexpected alignment file. > Whereas the output from clustal omega is perfect and the format what I need > is not given in the output option. > > Because I will be needing this .pir output file to model my target sequence > using modeller. > > thanks > > S.Jayashankar > Research Student > Institute for Biophysical Chemistry > Hannover Medical School > Germany. > > > On Tue, Mar 27, 2012 at 3:26 PM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > > Dear S. Jayashankar, > > have you tried the clustalw options '-convert -output=PIR'? This should > result in a pir-formatted output file. > > Tim > > On 03/27/12 10:18, Jayashankar wrote: >>>> Dear All, >>>> >>>> A bit offtopic question, >>>> >>>> Does any body know how can I get the PIR output of the aligned sequence >>>> from clustal omega. >>>> I have a full length protein solved, to give weightage during comparitive >>>> modelling, I use domains of the same/similar protein solved before. >>>> I expect an alignment something that looks like one below, and clustalw >>>> does'nt seems to work , but clustal omega does it. But there is no .pir >>>> format output. >>>> >>>> >>>> 1.cccccccccccccaaaaaaaaaabbbbbbbb >>>> 2.-------------------------------------bbbbbbbb >>>> 3.ccccccccccccc------------------------------ >>>> 4.------------------aaaaaaaaaaa-------------- >>>> >>>> >>>> Thanks >>>> S.Jayashankar >>>> Research Student >>>> Institute for Biophysical Chemistry >>>> Hannover Medical School >>>> Germany. >>>> > >> - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPccYEUxlJ7aRr7hoRAqT2AKDyz0fwVnqhp5DjiiocWz7VrI5IOgCgpxhL YfM5EJQt5e2WoEU7iILcDbI= =QNtR -----END PGP SIGNATURE-----
