chainsaw does just that
eleanor
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
Does chainsaw not the opposite? Pruning a coordinate file based on
non-conserved residues identified in a MSA?
Yuan has a MSA of known structures and a sequence he wants to add to
it. I am always keen to learn about alignment programs, it would be
great to know how to use chainsaw for this
3-d coffee and expresso will align sequences without structures with sequences
that do have structures in a structure-based sequence alignment:
http://www.tcoffee.org/Projects_home_page/expresso_home_page.html
perhaps this is along the lines of what Yuan is looking for?
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?
Hi Yuan,
You can use UCSF Chimera's Multalign Viewer tool to do this. Just
open your alignment
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
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
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
