﻿Basic:
This directory contains a basic example of UPlabel calculating 
an optimized labeling schedule from a given sequence.

To enable the user to easily verify the schedule that is computed, 
a special sequence was chosen that contains no co-labeling pairs.
For that purpose all unique pairs are separated by prolines and  
prolines have been excluded from labeling scheme.

To get a better overview over the number of unique pairs and their 
occurrence in the the sequence the showuniquepairs command is used.
The multipair argument shows all unique pairs with an occurrence lower
than the supplied number.

The output is written to several files. One to read it back into 
UPlabel later and three human readable presentations. 

The calculation with a maximum number of samples of 3 is in tst_basic.cya.

Edit:
This example shows how to edit a labeling schedule by modifying pairs.

The showuniquepairs command shows the unique pairs in the sequence.
 On invocation all pairs are listed. It is shown how many times a 
pair occurs in the included sequence and how many times it appears 
in the whole sequence. The shortcut "banscramble" automatically bans
 PRO, ASP, ASN, GLU and GLN.

There are ten slots for labeling schemes, 5 of which are shown with 
the showmultiple command side by side. With the copyschedule schedules 
can be saved before or after editing with modifypair. The sched argument
 to modifypair codes for a labeling pattern. Since there are 2^samples 
labeling patterns the schedule pattern is described by a number ranging
 from 1 to 2^samples. For example the pattern X-X would be expressed by 
the number 5. The rank specifies the slot where the labeling should be edited.

The calculation is in the file tst_score.cya.

Price:
This directory contains an extended example of a UPlabel calculation
given the amino acid sequence and amino acid prices.

The amino acids are assigned high prices to make them unfavorable 
to the labeling scheme. The amino acids ALA, GLY and PRO are 
disfavored. To enable the incorporation of prices priceweight has to 
be unequal to zero. If the resulting labeling scheme is compared
to the scheme in the folder tst_basic. 

The calculation with a maximum number of samples of 3 and the 
incorporation of amino acid prices is in tst_prices.cya

Score:
This directory contains a more advanced example of UPlabel calculating 
an optimized schedule from a given sequence using labels and markers. 

For this example the cyana demo sequence was chosen. The label line 
supplies how much more a pair in the specified part of the sequence 
is worth than a pair with labeling score=1. 

The marker enables the user to speciy that a part of the sequence can 
be distinguished from the rest with another experiment or seperate 
Information. This can also be the difference in linewidth inside a 
membrane region to a region outside the membrane.

