4.1. How this Tutorial is Organised

EMBOSS contains more applications than can be covered in a short tutorial. This will introduce some of the applications and show you how to find out about the others.

Text you can expect to see on screen is highlighted but in some cases program output is truncated to save space. The Unix prompt is represented as %; you don't need to type this in! The commands you need to type are printed in bold. If no command is specified after a prompt, just press <RETURN>. Pressing <RETURN> will also dismiss graphics windows.

4.1.1. wossname: a first EMBOSS Application

All EMBOSS programs run from the Unix command line. The EMBOSS utility wossname will produce a list of all the EMBOSS applications.

4.1.2. Exercise: wossname

Type wossname at the % prompt. EMBOSS programs start up with a one line description and then prompt you for information. In this case you'll see:

% wossname
Finds programs by keywords in their one-line documentation
Keyword to search for: protein

antigenic     Finds antigenic sites in proteins
backtranseq   Back translate a protein sequence
checktrans    Reports STOP codons and ORF statistics of a protein sequence
emowse        Protein identification by mass spectrometry
digest        Protein proteolytic enzyme or reagent cleavage digest
eprotdist     Protein distance algorithm
eprotpars     Protein parsimony algorithm
fuzzpro       Protein pattern search
fuzztran      Protein pattern search after translation
garnier       GARNIER predicts protein secondary structure.
iep           Calculates the isoelectric point of a protein
octanol       Displays protein hydropathy
oddcomp       Finds protein sequence regions with a biased composition
patmatdb      Search a protein sequence database with a motif
patmatmotifs  Search a motif database with a protein sequence
pepnet        Displays proteins as a helical net
pepstats      Protein statistics
pepwheel      Shows protein sequences as helices
pepwindow     Displays protein hydropathy
pepwindowall  Displays protein hydropathy of a set of sequences
preg          Regular expression search of a protein sequence
pscan         Scans proteins using PRINTS
sigcleave     Reports protein signal cleavage sites
topo          Draws an image of a transmembrane protein

Many EMBOSS programs have additional, optional parameters that offer more functionality. As a rule, you can force the program to present this information to you by appending the flag -options to the program name as shown below. You will be presented with a variety of additional options. The default value for each option is given in square brackets, and you can either press <RETURN> to accept the default, or enter the value you require:

% wossname -options
Keyword to search for: protein
Output program details to a file [stdout]: myfile
Format the output for HTML [N]: Y
String to form the first half of an HTML link:
String to form the second half on an HTML link:
Output only the group names [N]:
Output an alphabetic list of programs [N]:
Use the expanded group names [N]:

This set of commands will cause wossname to write out the list of programs to a file called myfile, in HTML format ready for viewing in a web browser.

To produce a list of all the current EMBOSS programs, start up wossname again but instead of specifying a keyword, press <RETURN>. A list of programs will scroll onto your screen, divided up into groups according to their functions. Scroll up and down to see them all. Can you think of how to get this data into a file? (Hint: use -options).

If you add the flag -help after the name of any EMBOSS program you will see a list of all the command flags available for this program. For example:

wossname -help

You'll see some more flags later.