In fact, it writes out not just the name of the sequence, but also the start and end position of a region within that sequence and, if the sequence is nucleic, if can specify whether the sequence is the reverse complement.
Without the program yank you would need to use a text editor such as pico to create the appropriate list files. yank makes this process easy.
Instead of containing the sequences themselves, a List file contains "references" to sequences - so, for example, you might include database entries, the names of files containing sequences, or even the names of other list files. For example, here's a valid list file, called seq.list:
unix % more seq.list opsd_abyko.fasta sw:opsd_xenla sw:opsd_c* @another_list
This looks a bit odd, but it's really very straightforward; the file contains:
Notice the @ in front of the last entry. This is the way you tell EMBOSS that this file is a list file, not a regular sequence file.
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You will be prompted for the start and end positions you wish to use.
If the sequence is nucleic, you will be prompted whether you wish to use the reverse complement of the sequence.
The output list file can now be read in by a program such as union by specifying the list file as '@cds.list' when union prompts for input.
The program extract does not make list files, but creates a sequence from sub-regions of a single other sequence.