EMBOSS: General Documentation

User Documentation

Tutorial

Every document on EMBOSS seems to have a section titled What is EMBOSS? This gentle tutorial by Val Curwen and others is no exception. It will lead you through using EMBOSS by showing you some of the more useful and ubiquitous programs in the package and allow you to investigate the properties and feel of the programs when run at the UNIX command-line.

Getting started with EMBOSS tutorial (or download ps)

Running EMBOSS Programs

EMBOSS programs are run by typing them at the UNIX prompt.

Any required information that you have not already given on the command-line will be prompted for.

The EMBOSS command syntax follows normal UNIX command conventions, (options start with a '-', for example: "program -format 2").

If in doubt, type:
programname -help to get some help on the options
or
programname -opt to make the program prompt you for common options
or
tfm programname to get the full help on a program

Interfaces

Some Graphical User Interfaces and Web Interfaces are being developed.

You might like to try running the cheerful little character-based menu program emnu.

Jemboss is a Java interface that is actively being developed at the HGMP.

There is a W2H interface available.

There are several other Web interfaces being developed:
http://corba.ebi.ac.uk/cgi-bin/alweb2/alweb.start?CFG=Emboss
http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html
http://ubigcg.mdh4.mdc-berlin.de:8080/
http://www-alt.pasteur.fr/~letondal/Pise/
http://sol.biol.unlp.edu.ar/wEMBOSS (Try it here)

There are also X-Windows interfaces being developed by various groups, for example:
http://userpage.fu-berlin.de/~sgmd/ (Kaptain)
http://www.bioinformatics.org/genpak/ (Arka)

Uniform Sequence Addresses

The Uniform Sequence Address, or USA, is a somewhat tongue-in-cheek reference to a URL-style sequence naming used by all EMBOSS applications.

The USA syntax is one of:

The "::" and ":" syntax is to allow, for example, "embl" and "pir" to be both database names and sequence formats. Everything to decode these is in one source file within the AJAX library.

In addition, EMBOSS allows the command line to separately define the format and the entry name so that only the filename is required

If all else fails, EMBOSS will guess the sequence format by trying all known formats until one succeeds.

Mailing Lists

Bug reports should be sent to the EMBOSS Support Team emboss-bug@embnet.org

In addition, you can join the EMBOSS users mailing list: