Any GCG program showing the prompt 'sequences(s)' can be given a list of sequence names, in a file, as the search-set. This is called a file of sequence names (FOSN). The FOSN should contain a list of sequence-file names and/or database entries, and can be created using an editor. Eg: Create a file called MYRNA.LIS which contains the following lines:
EMBL:*RNA*
MYRNA1.SEQ
GENBANK:D01457
ALIGNED.MSF{*}
When prompted, the filename is prefixed with '@'.
Search for query in what sequence(s) ? @MYRNA.LIS
All the files and/or database entries named in the FOSN will be analysed. Suitable FOSN's are created by GCG programs such as STRINGSEARCH and FASTA.
A Multiple Sequence File (MSF) contains several sequences within one file. This is unlike a FOSN, which only refers to a sequence indirectly. To indicate that an MSF file is being specified, use curly braces after the file name. Within the curly braces place a * to mean all the sequences in the MSF file.
Search for query in what sequence(s) ? ALIGNED.MSF{*}
An MSF file is produced by the GCG program PILEUP and the GCLUSTALV program.