Re: [ccp4bb] Sequence Alignment Question
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 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
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 wrote: From: Yuri 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
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
Re: [ccp4bb] Sequence Alignment Question
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
Jalview is another option. http://www.jalview.org/ Sent from my HTC - Reply message - From: "Yuri" Date: Fri, Aug 19, 2011 00:31 Subject: [ccp4bb] Sequence Alignment Question To: 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
Thanks everyone, for the help. -- Yuri Pompeu