Dear Tim, Thanks, The Jalview, output to textbox in PIR worked thr trick.
S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Tue, Mar 27, 2012 at 3:52 PM, Tim Gruene <[email protected]> wrote: > -----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 <[email protected]> > 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----- >
