Dear Yuan, the MUSCLE program can do that for you. It is capable of doing profile-profile and profile-sequence alignments.
http://www.drive5.com/muscle/muscle_userguide3.8.html#_Toc260497021 Section 2.10 of the manual should be what you want. Cheers, Thomas On Mon, May 31, 2010 at 01:46, Tim Gruene <[email protected]> wrote: > Dear Yuan SHANG, > > you can use Jalview do create and edit an alignment with your sequence. > Jalview is available at http://www.jalview.org/, and I quite liked it when I > worked with it. > > Tim > > > On Mon, May 31, 2010 at 04:29:48PM +0800, 商元 wrote: >> Hello, everyone, >> I've a protein sequence of known domain. Based on structure alignment, >> I've got a alignment of those with known structures. Then how to add my >> sequence to the alignment?Any suggestions? >> Regards, >> Yuan SHANG > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > > iD8DBQFMA3djUxlJ7aRr7hoRArVqAJsGxH8tcPIzwtzpeGFSB7yNGWLBNACg3wbj > 5hpD2QWQG6h3X6ySCViGxDc= > =0qUC > -----END PGP SIGNATURE----- > >
