Introduction to EMBOSS

EMBOSS

EMBOSS is a suite of programs developed to do molecular biology by EMBnet. EMBOSS is free software and although it is primarily developed for Linux it also runs in MS Windows and Mac OS X.

EMBOSS is comprised by hunders of programs and includes utilities to align sequences, translate RNA to proteins, identify protien motifs, analyze repetitions, calculate codon usage statistics and many more analyses.

Running EMBOSS commands

The EMBOSS utilities have a Command Line Interface and all can be run from a text terminal. The documentation for the EMBOSS aplications is written taking into account mainly the Command Line Interface.

But there are other ways to run the EMBOSS software.

You can use emboss online in the Wageningen server.

There are web servers that provide the EMBOSS tools as a service. In those servers the EMBOSS utilities can be accessed as web pages and the server runs the terminal command and return the result.

Another interface to EMBOSS is Jemboss. Jemboss is a Graphical User Interface application, like any of the other common desktop applications.

Identify the command

When we do not know which of the EMBOSS commands to use we can use another EMBOSS command, wossname, to search in the EMBOSS command list.

Get a list with all commands:

$ wossname

Look for command to do alignments:

$ wossname alignment

Getting help for a command

The command manuals can be found in the web.

They are also available in any EMBOSS installation by using the tfm command. For instance, to read the manual for the water command we could run:

$ tfm water

The manual reader is similar to the Unix less command.

It is also possible to get a brief list of parameters available with the option “-help” and the complete list with “-help -verbose”

$ water -help -verbose

Example: change a sequence format

To get familiar with the EMBOSS way of running the analyse we will change the format of a sequence file. EMBOSS has a program to modify sequence files: seqret

seqret can change the sequence format, trim the sequences and reverse-complement them. Let’s change the format of fasta sequence file to the GenBank format.

If we run seqset in the command line it will ask for the input file and for the output file:

$ seqret

By default seqret won’t change the sequence format unless we specify the output format that we want. To do it we have to write genbank::secuencia.gb. We can also tell seqret which is our input file:

$ seqret secuencia.fasta genbank::secuencia.gb

We could sent the result to standard output instead of a file. This is a general feature of all EMBOSS programs.

$ seqret secuencia.fasta genbank::stdout

To reverse and complement a sequence we can use the parameter -sreverse1:

$ seqret secuencia.fasta embl::stdout -sreverse1

Would the result sequence be different in this case?

seqret can also trim the input sequence.

$ seqret secuencia.fasta embl::stdout -sbegin1 10 -send1 30