EMBOSS

From CLAB

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.

Contents 1 Availability 2 GUIs 3 Documentation/Tutorial 4 Linux Installation Procedure 4.1 Additional Integrated Tools and Datasets 4.1.1 Comparing to GCG datasets

[edit] Availability

• klab.ist.unomaha.edu (6.0.1)

---

• biobase.ist.unomaha.edu (?)

---

• phylogeny.ist.unomaha.edu (6.1.0)

[edit] GUIs

• EMBOSS explorer - Perl
  • Local install: http://biobase.ist.unomaha.edu/ee/
• jEMBOSS - Java
  • Click here to use via your web browser. (You will need a username and password -- Contact Us.)
  • Windows Installer
• wEMBOSS - Perl & C
• ... and a dozen other GUI/Web interfaces?

[edit] Documentation/Tutorial

• 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
• Emboss_tutorial
• Design of JEMBOSS

[edit] Linux Installation Procedure

This seems to work now:

apt-get install emboss

But if that doesn't work for you, keep reading.

Mohammad wrote EMBOSS / jEMBOSS install instructions and attached them to RT 220.

$ 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 /usr/local/bin)

You can now install "EMBASSY" applications like HMMER and PHYLIP if you like.

[edit] Additional Integrated Tools and Datasets

Each of these have their own EMBOSS related installation procedures.

• Tools
  • PHYLIP
  • HMMER
• Datasets
  • Genbank
  • REBASE
  • UniProt (aka UniProt Knowledgebase Release, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL)
  • PROSITE
  • Pfam

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.

[edit] Comparing to GCG datasets

My notes about GCG vs. EMBOSS datasets. --Jhannah 14:24, 5 January 2009 (CST)

They may be doing some interesting things at UCSF and ym.edu.tw?

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[1]               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)

1. 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"