Trace_diff is a program for automatic detection of point mutations. It has a command line interface and is normally run from a script such as pregap (see section Pregap4 introduction) to operate on a batch of sequences. Usually the file to be scanned for mutations will be an experiment file which contains the name of its own trace file and the name of a file containing the reference trace. The readings' trace is aligned with that of the reference, and bases that differ and have significant trace differences are tagged as possible mutations. Trace_diff calculates the mean and standard deviation of the difference trace, and the "significance" of the trace differences is defined in standard deviation units. The user specifies the threshold using the -n option. When a possible mutation is found trace_diff writes a MUTN tag to the readings experiment file. The tag text contains an NC-IUB code (see below) to define the change, e.g. Y = C to T change and y = T to C change, and a numerical value gives the corresponding peak height in sd units.
NC-IUB SYMBOLS USED BY TRACE_DIFF A,C,G,T r (A,G) 'puRine' y (T,C) 'pYrimidine' w (A,T) 'Weak' s (C,G) 'Strong' m (A,C) 'aMino' k (G,T) 'Keto' R (G,A) 'puRine' Y (C,T) 'pYrimidine' W (T,A) 'Weak' S (G,C) 'Strong' M (C,A) 'aMino' K (T,G) 'Keto'
The options are described below.
-o. Valid values are
3. Defaults to
16. Defaults to
-e) should be clipped, if necessary, by the
QRline types in the experiment file. Hence the start position is the maximum of the
-svalues, whilst the end position in the minimum of
Examples 1. Get the usage. arran % trace_diff trace_diff v1.06 Copyright (c) MRC Laboratory of Molecular Biology, 1997. All rights reserved. Usage: trace_diff [options] file [wildtype-file] Where options are: [-b band width (def. 30)] [-p precision (8|16)] [-v version (2|3)] [-n num_sd (def. 4.000000)] [-s start (def. 50)] [-e end (def. 300)] [-o output file] [-S] [-c] [-a] 2. Run trace_diff on the file hs0091 using the quality clip points (the QL and QR values) or 45 and 500, whichever gives the narrowest range, and a threshold of 2.9. arran % trace_diff -n2.9 -s45 -e 500 -c hs0091