[ Previous chapter ][ This chapter ][ Next chapter ] Reformatting tools have been described earlier . Do not mix up 'reformatting' in the GCG sense with 'importing' - the functionality might seem similar but an 'import' process is much more dangerous in terms of potential data loss.
The GCG software can tell you all options available with the
check
option applied to the program 'reformat'. This includes
RNA, DNA, MSF file, FOSN file format, and mixed-case or
all-uppercase or all-lowercase sequence
data.
% reformat -check
Upon closer inspection
of the GCG format, you might notice that
the
sequence type
is recorded
as part of the sequence. If you encounter problems
in sequence handling, and are suspiciously
assuming that 'the computer is wrong',
make sure that the type of sequence is recoreded properly.
Nucleotide sequences
are determined to be non-protein if the GATC-content is beyond a certain
threshold.
The following options apply to the
reformat
program:
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Subsection 7.4.2 Problems in reformatting
-PROtein insists that the sequences are reformatted as
protein sequences
-NUCleotide insists that the sequences are reformatted as
nucleic acid sequences