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14.1. Using files of sequence names

You will have noticed the different ways in which a "database" can be defined in GCG. One way is simply to have a file of references to sequences: a "file of sequence names" (FOSN). Eg: create a file called mytest.fil containing these lines:

@myoglobin.strings
*.embl
platelet.seq

When running FASTA, or other database-search programs, @MYTEST.FIL is given in place of a database name. This makes it very easy to manage a database. You need only keep a directory containing your personal sequences, and a list pointing to those sequences.

This is not sufficient for the STRINGSEARCH program, as any text in your personal data will not have been indexed. To do this, you must run DATASET which builds a whole database.

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