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: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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/ > > iD8DBQFPccAdUxlJ7aRr7hoRAh2BAJwP6HdQd6t0/TVZBLZCA/S4KEMY9wCeM2WL > 7R/ULzOB+kq8fltCbQ6EUR4= > =fzmD > -----END PGP SIGNATURE----- >
