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> will also dismiss graphics windows.
All EMBOSS programs run from the Unix command line. The EMBOSS utility wossname will produce a list of all the EMBOSS applications.
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:
wossnameFinds programs by keywords in their one-line documentation Keyword to search for:
proteinSEARCH 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 -optionsKeyword to search for:
proteinOutput program details to a file [stdout]:
myfileFormat the output for HTML [N]:
YString 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
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:
You'll see some more flags later.