This module compares each sequence chromatogram against a "wild type" or
reference chromatogram to detect point mutations. The wild type file may be
any normal trace from a standard comparator sequence or may be produced by
averaging the traces of all the chromatograms (which can presently only be
done in Gap4, thus requiring two runs of Pregap4 and Gap4). The mutations are
detected by aligning and subtracting each trace from the wild type trace to
produce a "difference trace". The difference trace is then analysed to
identify point mutations which are written back to the Experiment File and
MUTN tags. This uses the
trace_diff program (see section Introduction to mutation detection).
Bonfield, J.K., Rada, C. and Staden, R. Automated detection of point
mutations using fluorescent sequence trace subtraction. Nucleic Acids Res. 26,
- Option: Wild type file
This is the filename of the chromatogram for the wild type sequence. This may
be in SCF, ABI or ALF format.
- Option: Start position
- Option: End position
These define the range within each sequence in which to identify mutations.
The algorithm works better on good quality data so including very bad sequence
may give errors.
- Option: Score
This a threshold used to determine when a peak in the difference trace is
considered to be a mutation. The higher the value the more stringent the test.
- Option: Alignment band width
The trace alignment is performed by firstly doing a sequence alignment on the
text sequences contained in the two files. This specifies the band width for
this alignment. Smaller values give quicker alignments, but only work if the
alignment is sufficiently close to the main diagonal.
- Option: Other arguments
This allows for any other arguments to be passed to the
program. See the trace_diff documentation for more details.
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Last generated on 2 Febuary 1999.