EMBOSS is a open source software analysis package consisting of about 100 different sequence analysis programs. It includes a set of core software libraries (AJAX and NUCLEUS) for bioinformatics software developers.
Click here for one quick and easy way to get started using your web browser. More powerful interfaces are available below in case you find you need them.
- klab.ist.unomaha.edu (6.0.1)
- biobase.ist.unomaha.edu (?)
- phylogeny.ist.unomaha.edu (6.1.0)
- EMBOSS explorer - Perl
- Local install: http://biobase.ist.unomaha.edu/ee/
- jEMBOSS - Java
- wEMBOSS - Perl & C
- ... and a dozen other GUI/Web interfaces?
- Introduction to Sequence Analysis using EMBOSS
- Application Group To use EMBOSS you may need to make your self familiar with a new set of program names. This page contains a list of all such program names
- Design of JEMBOSS
Linux Installation Procedure
This seems to work now:
apt-get install emboss
But if that doesn't work for you, keep reading.
$ apt-get install libplplot-dev (to avoid this problem) $ cd src $ wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.1.0.tar.gz $ tar xvzf EMBOSS-6.1.0.tar.gz $ cd EMBOSS-6.1.0 $ ./configure $ make $ make install
EMBOSS is now installed in
/usr/local/share/EMBOSS (and 191 binaries into
Additional Integrated Tools and Datasets
Each of these have their own EMBOSS related installation procedures.
When you're done installing each of those you may want to sym link emboss.default as shown at the top of that file so that all users can use your new datasets.
Comparing to GCG datasets
My notes about GCG vs. EMBOSS datasets. --Jhannah 14:24, 5 January 2009 (CST)
GCG list from
gsaf.unmc.edu (in order of descending priority):
y GenBank Release 138.0 (10/2003) y Restriction Enzymes (REBASE) (09/2003) y SWISS-PROT Release 42.00 (10/2003) y SP-TREMBL Release 25.0 (10/2003) Pfam Release 10.0 (07/2003) via EMBASSY HMMER only PROSITE Release 18.08 (09/2003) same procedure as Pfam? y EMBL (Abridged) Release 76.0 (09/2003) GenPept Release 138.0 (10/2003) PIR-Protein Release 77.08 (08/2003) NRL_3D Release 28.0 (01/2001)
- ehmmpfam says "hmmfile will be looked for first in the current working directory, then in a directory named by the environment variable HMMERDB. This lets administrators install HMM library(s) such as Pfam in a common location"