Type wossname at the unix % prompt:
unix % wossname
EMBOSS programs start up with a one line description and then prompt you for information; in this case you see:
Finds programs by keywords in their one-line documentation
Keyword to search for: protein
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 |
unix % wossname -opt
You will now 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:
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 -opt)
If you append the flag -help to the name of any EMBOSS program
you will see a list of all the command flags available for this
program. For example:
unix % wossname -help
We'll see some more flags later. Let's move on to some sequence analysis ...