4.8. Conclusions

You have seen some of the programs available within EMBOSS, and have been introduced to the way you can run these programs from the command line. You have not explored all the options available with these programs, and certainly have not completely covered all the applications currently available. This tutorial should have taught you a little about EMBOSS, and you should now have a better idea of the types of problems it can help you to solve.

You are encouraged to visit the EMBOSS web pages at http://emboss.open-bio.org/ where you will find information on the various applications EMBOSS has to offer. There is also a manual built into EMBOSS known as tfm.

4.8.1. Exercise: tfm

You can use this program to see the manual entries for each program in EMBOSS. Let's look at the entry for the program wossname:

% tfm wossname

Displays full documentation for an application



   Finds programs by keywords in their short description


   wossname search for the specified keywords (or parts thereof) in the
   application short description (as displayed by a program when it
   starts), functional group name and keywords. The group name,
   application name and short description of any matching applications is
   output (screen by default). If no search words are specified, then
   details of all the EMBOSS programs are output. There are various
   options for controlling how the search is performed and what is given
   in the output file. Optionally, the output will be wrapped in HTML
   tags ready for inclusion in a Web page.



The program displays the contents of the manual page by page, and you can move onto the next page by using the space bar. This behaviour may be turned off using the -nomore option.