at the MPI

Questions and Answers to EMBOSS - the European Molecular Biology Open Software Suite

Table of Contents:

What is EMBOSS?
Who is our local EMBOSS manager?
On which computer-systems is EMBOSS running?
How can I start EMBOSS?
How can I get help on EMBOSS?
Which databases are installed inside the EMBOSS suite?
How can I specify sequences for EMBOSS?
How can i see the graphic output?

What is EMBOSS?

EMBOSS is a new suite of freely available programs and libraries for sequence analysis. It incorporates and integrates a range of currently available public packages and tools into a general, publicly available, suite specially developed for the needs of the Sanger Centre and the EMBnet user community.

History
Since 1988, the sequence analysis package EGCG has provided extensions to the market leading commercial sequence analysis package GCG. EGCG development was a collaboration of groups within EMBnet and elsewhere.
That project has reached the limits of what the authors can achieve using the GCG package. Specifically, it is no longer possible to distribute academic software source code which uses the GCG libraries and has become difficult even to distribute binaries. As a result, the former EGCG developers have been designing a totally new generation of academic sequence analysis software. This has resulted in the present EMBOSS project.

Inside EMBOSS you will find more then 200 programs around the sequence analysis (see also here):

Alignment
Coding regions
Comparison

CpG islands
Database entry extraction
Database information

Display alignment multiple
DNA sequence composition
DNA sequence features

DNA sequence properties
Enzyme kinetics
Gene finding

Hydropathy
Motifs
Mutation

Pattern matching
Primers
Profiles

Protein sequence composition
Protein sequence features
Protein sequence properties

Reformatting
Repeats
Restriction enzymes

Secondary structure
Sequence comparison
Sequence composition

Sequence display
Sequence editing
Sequence information

Site directed mutagenesis
Text search
Transcription

Translation
Utilities
Utilities keyword search

Who is our local EMBOSS manager?

The EMBOSS suite is managed by Alfred Beck

On which computer-systems is EMBOSS running?

EMBOSS is running on all Linux systems. You can use there tata (Linux 64 bit) as a public servers. Other system are also available for dedicated departments or groups.

How can I start EMBOSS?

The command "EMBOSS" starts EMBOSS as a new shell. The current release ist 6.1.0.
If you prefer a graphical interface use can use the Jemboss-Version of the packe with the command: "/package/emboss/runJemboss.sh" or if you like you can use it from a WEB-browser: http://booster.molgen.mpg.de:12055/Jemboss/ (you need Java Web Start for this).

How can I get help on EMBOSS?

Click here for a alphabetic sorted list of the programs or here for a list sorted by program groups.

You can also have a look to the offical EMBOSS page. Here you will find also a tutorial and here you find a Quick Guide in PDF-format.

And here are all EMBASSY programms:
domainatrix, domalign, domsearch, emnu, esim4, hmmernew, iprscan, memenew, mse, myembossdemo, phylipnew, signature, structure, topo and vienna.

On two ways you may get on-line help:

All programs accept the command line qualifier "-help" or "-help -verbose". This gives some more information about program options

The command "wossname -auto" or "wossname -alphabet -auto" give you a short list of available programs. With "tfm programname" you get the complete documentation on "programname".

Which databases are installed inside the EMBOSS suite?

EMBOSS is able to access the GCG-databases, so you will have the same database as inside GCG. Additionally is EMBOSS configured to access the EMBL SRS-Server to get some database from there.
You can get a list of all installed databases with the command "showdb".

How can I specify sequences for EMBOSS?

One of the advances of EMBOSS is wide range of supported file formates: IntelliGenetics, Genbank, NBRF, EMBL, GCG, DNAStrider, Fitch, FASTA, Phylip, PIR, MSF, ASN.1, PAUP, ClustalW.
EMBOSS use a Uniform Sequence Address system called "USA". The syntax is one of (see the two ":" after format):

"format::file"

"format::file:entry"

"dbname:entry"

Examples:

gcgpir:a1hu	Entry A1HU from GCGs NBRF/PIR library
fasta::myfile.seq	a local file in fasta format (see the two ":" after fasta)
gcg::mygcgfile.gcg	a local file in GCG format (see the two ":"after gcg)

But refer for more information to the description of the Uniform Sequence Address and to the description of the sequence formats.

How can i see the graphic output?

EMBOSS can support a number of different graphics output types. It will prompt for a graphics device (if you type rubbish, you will get a list of available devices) e.g.:

postscript (default) - this will create a file in postscript format. You can send this file with the unix command "lpr" to your favorite postscript printer or you may view it with "gv" (goastview, need a X-server on your workstation).

x11 - displays it on a extra X-Window on your workstaion. This works only if your display use not more than 256 colours!! Then you can try xterm.
For example: the Hummingbird Exceed X11 emulator (and maybe other systems) use the 'TrueColor' display by default.
You should change the configuration settings so that it uses 'PseudoColor'. In version 6.1 of Hummingbird Exceed, this is done by clicking on the Exceed tool bar at the bottom of the screen. Select 'Tools', then 'Configuration', then Screen Definition. A window will appear.
In the 'Server Visual' popup menu on the left, select 'PseudoColor'. Click on 'OK'.
With X-Win32 (StarNet) you must start the xwin32 configuration. Select others in the tab-bar and mark "PseudoColor Mode" and "Use Reverse Colors".

xterm - prints the grafik in a extra window.

png - Output the graphic to a PNG image file. You can include this file into modern graphic programs and web-browser.

The default names for output file are "programname.format" eg. "dottup.ps" as postscriptfile from the program "dottup".