Re: [ccp4bb] Alignment software
Another alignment tool worth to keep an eye on is this one: http://foldit.wikia.com/wiki/Alignment_Tool They are still debugging, but the plan is to release a standalone version after CASP9. Or at least a version that runs in a standalone FoldIt version. On Tue, May 25, 2010 at 15:18, Victor Alves vdal...@fmv.utl.pt wrote: Hi Charlie I am so sorry I assumed development had halted, but I'm glad one of the authors of ALINE has stepped in to restore the truth, and even more that ALINE is still being taken care of. Hopefully those needed funds will materialize, for your sake and also for the benefit of all the scientific community. I will e-mail you some suggestions. Cheers, Victor Alves __ VICTOR DIOGO ALVES, DVM PhD Professor Auxiliar Faculdade de Medicina Veterinária UTL - Lisboa __ -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Charlie Bond Sent: terça-feira, 25 de Maio de 2010 4:48 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Alignment software Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406
Re: [ccp4bb] Alignment software
Another tool you can use is RAPIDO (http://webapps.embl-hamburg.de/rapido). It identifies rigid bodies between the two structures and already produces pyMol scripts for the superposition both on the entire structure and on the single rigid bodies. A more complete list of the tools you can use can be found here: http://en.wikipedia.org/wiki/Structural_alignment_software
Re: [ccp4bb] Alignment software
Thanks Roger, that worked perfectly! I'll try and have fun with aline now. ciao, s On May 25, 2010, at 7:56 PM, Roger Dodd wrote: Hi there, I just got this working a couple of days ago under Mac OS X 10.6.3. I manually compiled and installed Perl-Tk from CPAN. Steps taken: 1. Download and ungzip / untar: http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz (the newer -503 version didn't work) 2. Change into the directory 3. Execute perl Makefile.PL 4. make 5. make test 6. sudo make install Hopefully that should get things working. Cheers, Roger On 25 May 2010 17:50, Sebastiano Pasqualato sebastiano.pasqual...@ifom-ieo-campus.it wrote: Hi there, I remember a friend of mine showing me Aline, and it looked very nice. However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3). With respect to the instruction I found on the website, I had to change the export lines to be added to the .bashrc in order not to get error messages. That's how I added the path info: export ALINEHOME='/sw64/share/xtal/aline_011208' export PATH=$PATH:$ALINEHOME/bin however, I still get an error while trying to run aline: s...@host005:~ aline Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 /sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /sw64/share/xtal/aline_011208/bin/aline line 37. BEGIN failed--compilation aborted at /sw64/share/xtal/aline_011208/bin/aline line 37. s...@host005:~ I even tried with the perl -MCPAN -e 'install Tk' command, as suggested by the website, but nothing changed. Any idea of what's wrong here? Thanks a lot for the tips, ciao s On May 25, 2010, at 5:47 AM, Charlie Bond wrote: Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406 -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990 -- Roger B. Dodd, PhD. Cambridge Institute for Medical Research Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY UK -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990
Re: [ccp4bb] Alignment software
Hi all. I'm rather surprised that Jalview has yet to be mentioned: http://www.jalview.org/ Although I've heard that ESPript can make the best looking figures, Jalview is also capable of generating very beautiful output, and I've found it reasonably intuitive and plenty powerful. I'm not fond of the command line, so the Jalview GUI is especially sweet for me. -Joel On Wed, May 26, 2010 at 2:13 AM, Sebastiano Pasqualato sebastiano.pasqual...@ifom-ieo-campus.it wrote: Thanks Roger, that worked perfectly! I'll try and have fun with aline now. ciao, s On May 25, 2010, at 7:56 PM, Roger Dodd wrote: Hi there, I just got this working a couple of days ago under Mac OS X 10.6.3. I manually compiled and installed Perl-Tk from CPAN. Steps taken: 1. Download and ungzip / untar: http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz(the newer -503 version didn't work) 2. Change into the directory 3. Execute perl Makefile.PL 4. make 5. make test 6. sudo make install Hopefully that should get things working. Cheers, Roger On 25 May 2010 17:50, Sebastiano Pasqualato sebastiano.pasqual...@ifom-ieo-campus.it wrote: Hi there, I remember a friend of mine showing me Aline, and it looked very nice. However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3). With respect to the instruction I found on the website, I had to change the export lines to be added to the .bashrc in order not to get error messages. That's how I added the path info: export ALINEHOME='/sw64/share/xtal/aline_011208' export PATH=$PATH:$ALINEHOME/bin however, I still get an error while trying to run aline: s...@host005:~ aline Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 /sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /sw64/share/xtal/aline_011208/bin/aline line 37. BEGIN failed--compilation aborted at /sw64/share/xtal/aline_011208/bin/aline line 37. s...@host005:~ I even tried with the perl -MCPAN -e 'install Tk' command, as suggested by the website, but nothing changed. Any idea of what's wrong here? Thanks a lot for the tips, ciao s On May 25, 2010, at 5:47 AM, Charlie Bond wrote: Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406 -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990 -- Roger B. Dodd, PhD. Cambridge Institute for Medical Research Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY UK -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990
Re: [ccp4bb] Alignment software
Hy Mohd, There was recently a nice review about all the alignment software available. You might find one you like in there. Visualization of multiple alignments, phylogenies and gene family evolution. http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.1434.html By the way there's also a review on structures visualization software in the same supplement issue about visualizing biological data, that might interest other readers form that list as well. Visualization of macromolecular structures. http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.1427.html Best, Luc -- Luc Bonnefond, PhD. Division of Structure Biology Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo bonne...@ims.u-tokyo.ac.jp l.bonnef...@gmail.com
Re: [ccp4bb] Alignment software
Thank you all for very helpful suggestions, I used the software STRAP, Espript is also user friendly and effective. Many recommended ALINE, but unfortunately I had troubles with the download. Thanks again, Mohd
Re: [ccp4bb] Alignment software
Hi there, I remember a friend of mine showing me Aline, and it looked very nice. However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3). With respect to the instruction I found on the website, I had to change the export lines to be added to the .bashrc in order not to get error messages. That's how I added the path info: export ALINEHOME='/sw64/share/xtal/aline_011208' export PATH=$PATH:$ALINEHOME/bin however, I still get an error while trying to run aline: s...@host005:~ aline Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 /sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /sw64/share/xtal/aline_011208/bin/aline line 37. BEGIN failed--compilation aborted at /sw64/share/xtal/aline_011208/bin/aline line 37. s...@host005:~ I even tried with the perl -MCPAN -e 'install Tk' command, as suggested by the website, but nothing changed. Any idea of what's wrong here? Thanks a lot for the tips, ciao s On May 25, 2010, at 5:47 AM, Charlie Bond wrote: Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406 -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990
Re: [ccp4bb] Alignment software
Hi there, I just got this working a couple of days ago under Mac OS X 10.6.3. I manually compiled and installed Perl-Tk from CPAN. Steps taken: 1. Download and ungzip / untar: http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz(the newer -503 version didn't work) 2. Change into the directory 3. Execute perl Makefile.PL 4. make 5. make test 6. sudo make install Hopefully that should get things working. Cheers, Roger On 25 May 2010 17:50, Sebastiano Pasqualato sebastiano.pasqual...@ifom-ieo-campus.it wrote: Hi there, I remember a friend of mine showing me Aline, and it looked very nice. However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3). With respect to the instruction I found on the website, I had to change the export lines to be added to the .bashrc in order not to get error messages. That's how I added the path info: export ALINEHOME='/sw64/share/xtal/aline_011208' export PATH=$PATH:$ALINEHOME/bin however, I still get an error while trying to run aline: s...@host005:~ aline Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 /sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at /sw64/share/xtal/aline_011208/bin/aline line 37. BEGIN failed--compilation aborted at /sw64/share/xtal/aline_011208/bin/aline line 37. s...@host005:~ I even tried with the perl -MCPAN -e 'install Tk' command, as suggested by the website, but nothing changed. Any idea of what's wrong here? Thanks a lot for the tips, ciao s On May 25, 2010, at 5:47 AM, Charlie Bond wrote: Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406 -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094 fax +39 02 9437 5990 -- Roger B. Dodd, PhD. Cambridge Institute for Medical Research Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY UK
Re: [ccp4bb] Alignment software
Salameh, Mohd A., Ph.D. wrote: Dear All, I'm trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd We found esprit very useful.. Eleanor But now I cant find the site!
Re: [ccp4bb] Alignment software
Title: Re: [ccp4bb] Alignment software I usually use Espript via the web interface. downloadable espript: http://espript.ibcp.fr/ESPript/ESPript/ or the web server: http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi hope it's of use, Paul.. ### Dr. Paul A. McEwan Office B55 Centre for Biomolecular Science University of Nottingham Nottingham NG7 2RD UK Tel: 0115 8232010 (office) Tel: 0115 8232011 (lab) http://www.nottingham.ac.uk/Pharmacy/Research/MCSB/StructuralBiology/index.aspx ### From: CCP4 bulletin board on behalf of Eleanor DodsonSent: Mon 24/05/2010 12:54 PMTo: CCP4BB@JISCMAIL.AC.UKSubject: Re: [ccp4bb] Alignment software Salameh, Mohd A., Ph.D. wrote: Dear All, I'm trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, MohdWe found esprit very useful..EleanorBut now I cant find the site! This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Re: [ccp4bb] Alignment software
Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406
Re: [ccp4bb] Alignment software
Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It's quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Salameh, Mohd A., Ph.D. Sent: sexta-feira, 21 de Maio de 2010 16:11 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Alignment software Dear All, I'm trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd
Re: [ccp4bb] Alignment software
I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd For those who like TeX, TeXshade is incredibly powerful, and produces beautiful alignment figures. http://www.ctan.org/tex-archive/help/Catalogue/entries/texshade.html James -- Dr. James W. Murray David Phillips Research Fellow Division on Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Victor Alves [vdal...@fmv.utl.pt] Sent: Sunday, May 23, 2010 12:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Alignment software Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Salameh, Mohd A., Ph.D. Sent: sexta-feira, 21 de Maio de 2010 16:11 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd
[ccp4bb] Alignment software
Dear All, I'm trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd
Re: [ccp4bb] Alignment software
Try ESPript.. Gauri
