Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment
Dear Wenhe, have you looked at http://www.jalview.org/ ? is this what you are looking for? http://www.jalview.org/examples/examples3.html ciao, Sebastiano On Feb 3, 2012, at 6:32 AM, WENHE ZHONG wrote: Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe alignment.png -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990
Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment
I'm pretty certain that Jalview http://www.jalview.org/ can do that (you might have to set the user defined colours yourself). Dave. David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk Webs : http://flavors.me/xtaldave Twitter: @xtaldave Skype: DocDCB On 3 February 2012 05:32, WENHE ZHONG wenhezhong.xmu@gmail.com wrote: Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe
Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Wenhe, clustalx exports to PostScript with colour coding according to conservation. seaview is another tool for that purpose. Tim On 02/03/2012 06:32 AM, WENHE ZHONG wrote: Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPK79EUxlJ7aRr7hoRAhsWAJ962PO53UIKdRP6iuzhD+YRm8R7/gCg9dPF 3c+dQQyXiNYGq7hwrUmLsDo= =glGv -END PGP SIGNATURE-
Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment
Dear Wenhe: Indonesia (Madsen, Johansson Kleywegt, 2002), http://xray.bmc.uu.se/~dennis/, also has multiple coloring and output format possibilities, including postscript, similar to your example. Ten years later, it's still easy to install and run (tested on Fedora Linux in the past month). Apart from the package itself, you just need to install Java Runtime Environment and give the input sequences in PIR format. Regards, Navdeep --- On Fri, Feb 03, 2012 at 05:32:08AM +, WENHE ZHONG wrote: Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe --- Navdeep Sidhu Department of Structural Chemistry University of Goettingen Tammannstr. 4 37077 Goettingen Germany Email: nsi...@shelx.uni-ac.gwdg.de Phone: +49 551 39 3066 Fax: +49 551 392 2582 Dept. Homepage: http://shelx.uni-ac.gwdg.de/ ---
Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment
Wenhe, Bioedit (http://www.mbio.ncsu.edu/bioedit/bioedit.html) is able to do this. You can also export a nice alignment as RTF file into Word from the graphics view. This comes in handy for publication and presentation. Cheers, Carsten From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of WENHE ZHONG Sent: Friday, February 03, 2012 12:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe
Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment
Hi Wenhe, if you have already your alignment file you could also load it in Charlie Bonds ALINE. The program allows to color by similarity in grayscale as well as in colour mode. Regards Christian Am Freitag 03 Februar 2012 06:32:08 schrieb WENHE ZHONG: Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe
Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment
Hello Wenhe, Have you tried using our free Discovery Studio Visualizer? http://accelrys.com/products/discovery-studio/visualization-download.php You can generate and color alignments using various properties like alignment similarity, chemical type, steric, and many others. In addition, you can select your own custom coloring for each property. I have attached a small screenshot of the view for your sample picture trying to match your coloring scheme. Cheers, Francisco Francisco Hernandez-Guzman, PhD, MBA Sr. Product Manager http://accelrys.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of WENHE ZHONG Sent: Thursday, February 02, 2012 9:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe attachment: sequence_alignment.jpg
[ccp4bb] off-topic: special format for multiple sequence (protein) alignment
Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe attachment: alignment.png
Re: [ccp4bb] off-topic: special format for multiple sequence (protein) alignment
On Thursday, 02 February 2012, you wrote: Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. That looks similar to the output of TeXshade, with the shading mode set to hydropathy. Ethan
