The lines of output information are guaranteed not to have trailing white-space at the end.
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
| Program name | Description |
|---|---|
| emma | Multiple alignment program - interface to ClustalW program |
| infoseq | Displays some simple information about sequences |
| plotcon | Plot quality of conservation of a sequence alignment |
| prettyplot | Displays aligned sequences, with colouring and boxing |
| seealso | Finds programs sharing group names |
| showalign | Displays a multiple sequence alignment |
| showdb | Displays information on the currently available databases |
| textsearch | Search sequence documentation. Slow, use SRS and Entrez! |
| tfm | Displays a program's help documentation manual |
| tranalign | Align nucleic coding regions given the aligned proteins |
| whichdb | Search all databases for an entry |
| wossname | Finds programs by keywords in their one-line documentation |