Searches for potential probe target sites within the sequence entries of the corresponding 'PT_SERVER' (not the current) database from a list of named probes in a probe collection. Matching is performed with the maximum allowable number of mismatches for each given probe.
Probe collections are created or loaded with the PROBE COLLECTION window. Probes must be named with unique names otherwise the match results cannot be reconcilled correctly. Similarly, species within the tree must also have unique names for the match processing to work correctly.
To add a probe to the collection enter the 'Target String' and the 'Probe Name' and press the ADD button. To remove a probe from the collection select the probe from the 'Probes' list and press the REMOVE button. Pressing the 'FORGET' button will remove all probes from the collection and start a fresh.
To save the probe collection to file press the 'SAVE' button and to load a previously created collection press the 'LOAD' button. Probe collections are stored in a simple XML format so they can be easily created with an external text editor. The file format is detailed below.
The 'Match Weighting' matrix specifies how mismatch penalities will be alloted to sequence mismatches. The 'Positional Weighting' parameters adjust the mismatch penalities according to position through the following equations:
S = -ln(10) / 'Width'
P = (((2.0 * 'position') - 'length') / 'length') - 'Bias'
Weight = exp(S * P * P)
where 'position' is the sequence position and 'length' is the probe length. weighting function gives a bell curve shape whose spread is controlled by the 'Width' parameter, centre is controlled by the 'Bias' parameter and whose maximum is one.
For the default values of 1 and 0 for 'Width' and 'Bias' respectively the weighting function has a value of 1 for a position that is half the probe length and 0.1 at the zeroth position and the probe length position.
The 'Match Weighting' and 'Positional Weighting' parameters are saved as part of the probe collection XML file.
The MATCH PROBES WITH SPECIFICITY window is used to perform probe collection matching. The 'Probes' list shows the probes in the probe collection to be matched. If the list is empty you can click on the EDIT button to open the PROBE COLLECTION window and create or open a probe collection. The CLEAR button clears any previous match results but leaves the probe collection in tact.
You need to select a 'PT_SERVER' from the menu displayed after pressing the 'PT_SERVER' button before you can carry out a probe collection match. Press the MATCH button to carry out the match operation. When the match is complete the number of matches found will be displayed and the complete list of match results can be viewed by pressing the RESULTS button. Be warned that with large probe collections this can be a very large text file.
Match results are displayed in the DENDROGRAM view using a series of vertical bars (one bar per probe) on the left hand side indicating regions in the tree where matches occur. Left mouse clicking on the bar will open a status message telling you which probe the bar corresponds to.