Re: [ccp4bb] Sequence Alignment Question

2011-08-19 Thread Murray, James W 
Re sequence alignment,

For those TeXnically inclined, TeXshade produces beautiful alignment figures. 
(Steep TeX learning curve, I have an example script if anyone wants one).

http://www.ctan.org/pkg/texshade

James

--
Dr. James W. Murray
David Phillips Research  Fellow
Division of Molecular Biosciences
Imperial College, LONDON
Tel: +44 (0)20 759 48895

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yuri 
[yuri.pom...@ufl.edu]
Sent: Friday, August 19, 2011 12:31 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Sequence Alignment Question

Hello Everyone,
A little off topic but, what is a good way to show (publication
quality) multiple sequence alignment?
I am trying to show conserved regions in related proteins from
different organisms.
Thank you
--
Yuri Pompeu

Re: [ccp4bb] Sequence Alignment Question

2011-08-19 Thread Daniel Ryan 
Jalview is another option.

http://www.jalview.org/

Sent from my HTC

- Reply message -
From: Yuri yuri.pom...@ufl.edu
Date: Fri, Aug 19, 2011 00:31
Subject: [ccp4bb] Sequence Alignment Question
To: CCP4BB@JISCMAIL.AC.UK

 UID 23435 BODY[1]0 {238}
Hello Everyone,
A little off topic but, what is a good way to show (publication 
quality) multiple sequence alignment?
I am trying to show conserved regions in related proteins from 
different organisms.
Thank you
-- 
Yuri Pompeu

Re: [ccp4bb] Sequence Alignment Question- Thank you everyone

2011-08-19 Thread Yuri 

Thanks everyone, for the help.

--
Yuri Pompeu

Re: [ccp4bb] Sequence Alignment Question

2011-08-18 Thread Vitali Stanevich 
You can try this site:
http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi

If you have .pdb for one of your sequences, you'll be able to show secondary
structure also.

vitali

On Thu, Aug 18, 2011 at 6:31 PM, Yuri yuri.pom...@ufl.edu wrote:

 Hello Everyone,
 A little off topic but, what is a good way to show (publication quality)
 multiple sequence alignment?
 I am trying to show conserved regions in related proteins from different
 organisms.
 Thank you
 --
 Yuri Pompeu

Re: [ccp4bb] Sequence Alignment Question

2011-08-18 Thread chandan kishore 
Use ALINE sequence editor. if you multiple sequence alignment file from 
clustalW, you can open in ALINE software and generate publication quality of 
image.

http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/  

--- On Thu, 18/8/11, Yuri yuri.pom...@ufl.edu wrote:

From: Yuri yuri.pom...@ufl.edu
Subject: [ccp4bb] Sequence Alignment Question
To: CCP4BB@JISCMAIL.AC.UK
Date: Thursday, 18 August, 2011, 5:31 PM

Hello Everyone,
A little off topic but, what is a good way to show (publication quality) 
multiple sequence alignment?
I am trying to show conserved regions in related proteins from different 
organisms.
Thank you
-- Yuri Pompeu

Re: [ccp4bb] Sequence Alignment Question

2011-08-18 Thread Edward A. Berry 

Yuri wrote:

Hello Everyone,
A little off topic but, what is a good way to show (publication
quality) multiple sequence alignment?
I am trying to show conserved regions in related proteins from
different organisms.
Thank you
--
Yuri Pompeu



or clustalw, e.g.

http://npsa-pbil.ibcp.fr/cgi-bin/align_clustalw.pl

You can save the HTML to your disk and edit it with mozilla (seamonkey),
print to pdf, or grab screenshot for a gif.
Color is limited to characters not background, which in my opinion looks
better anyway. One could use photoshop on the gif to color background -
but then maybe easier to use ESPript