protein similarities that plays a key role in many bioinformatics methods. It
contains about all currently published protein sequences and is continuously
updated.
The computational effort for keeping SIMAP up-to-date is constantly increasing.
Please help to update SIMAP by calculating protein similarities on your
computer.
WWW: http://boinc.bio.wzw.tum.de/boincsimap/
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.
WWW: http://bioperl.org/
PR: ports/93675
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.
WWW: http://bioperl.org/
PR: ports/93674
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
database) and is also available as a general purpose alignment editor.
WWW: http://www.jalview.org
PR: 93054
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
unnecessary PORTEPOCH bump)
- Update MASTER_SITES and WWW line, provide backup download site
- Come up with better port description
- Reset maintainer to ports@
- Uphold CXX and CXXFLAGS
- Clean up Makefile slightly
- Don't install yet another copy of GPL and texts in French
- Add SHA256 hash to distinfo
using sensitive, selective and rapid similarity searches of protein and
nucleotide sequence databases.
PR: ports/69636
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
L-system Explorer is a program used for viewing and creating
L-system fractals.
The following features are supported:
- Over 500 builtin L-systems, arranged into about 20 groups.
- Ability to create and save custom L-systems and L-system groups.
- Abilty to save images of L-systems (in PNG or JPEG format).
- Multiple L-systems can be viewed at the same time.
- Able to use custom colors and gradients.
- Can also generate random gradients, or completely random colors.
- Able to draw using lines, points, or a random combination of both.
PR: iports/51400
Submitted by: David Yeske <dyeske@yahoo.com>
allowing to analyse several proteins at the same time. The proteins can be
superimposed in order to deduce structural alignments and compare their
active sites or any other relevant parts. Amino acid mutations, H-bonds,
angles and distances between atoms are easy to obtain thanks to the
intuitive graphic and menu interface.
Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated
homology modelling server developped at Glaxo Welcome Experimental Research
in Geneva. Working with these two programs greatly reduces the amount of work
necessary to generate models, as it is possible to thread a protein primary
sequence onto a 3D template and get an immediate feedback of how well the
threaded protein will be accepted by the reference structure before
submitting a request to build missing loops and refine sidechain packing.
Swiss-PdbViewer can also read electron density maps, and provides various
tools to build into the density. In addition, various modelling tools are
integrated and command files for popular energy minimisation packages can be
generated.
Finally, as a special bonus, POV-Ray scenes can be generated from the
current view in order to make stunning ray-traced quality images.
WWW: http://www.expasy.ch/spdbv/
PR: 33902
Submitted by: chuynh@biolateral.com.au
