The standard file

To normalize the band positions from image coordinates to standardized band positions that can be matched against in a database, we need the pattern of a "master" marker lane, to calculate distortion factors, for the gel. The band positions of the marker bands of this "master" lane are kept in the standard file.

This is an example of a standard file

	STANDARD
	0    69.0  0.9  1000000
	755  261   0.9  23130
	781  265   0.9  21226
	940  305.0 0.9  12216
	976  313.0 0.9  11198
	1018 323.0 0.9  10180
	1048 332.0 0.9  9416
	1071 334.6 0.9  9162
	1126 349.0 0.9  8144
	1195 368.0 0.9  7126
	1235 381.0 0.9  6557
	.
	.
	.
	2626 822.3 0.9  1018
	2684 839.8 0.9  947
	2764 870.0 0.9  831
	2982 948.0 0.9  564
	3029 965.3 0.9  517
	3147 1007.7 0.9 396
	3202 1027.3 0.9 344
	3252 1046.5 0.9 298
	3333 1088.7 0.9 220

The first column contains the positions of the marker bands on the original master gel. Everything is mapped back to these positions.
The second column contains the positions of the actual standard bands used at the moment - If the marker set gets distorted due to a change in chemistry over the years, this second column can be adapted to contain a pattern that matches the current marker lanes better than the original pattern.
The third column are confidence values for these bands - 0.99 means that this band will always be there and must be matched and 0.01 means that it is highly unlikely that this band was called and might be ignored for matching.
The fourth column (optional) : contains the size of that marker fragment. This column isn't written when a standard file is created in step 4, but it can be added later (in a text editor) once the sizes are known.
When this data exists and the gel is normalized a file gelnumber.sizes is written in addition to the gelnumber.bands file, which contains the fragment sizes for each band, rather than the normalized migration distance as in the *.bands file

The "Viterbi" algorithm will try to match each position in this second column against the band positions in each marker lane, and the results can be viewed in Step 4.