source: trunk/HELP_SOURCE/source/probespec.hlp

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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      pt_server.hlp
5
6#Please insert subtopic references  (line starts with keyword SUB)
7
8# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
9
10#************* Title of helpfile !! and start of real helpfile strunk ********
11TITLE           Probe Collection Matching
12
13OCCURRENCE      ARB_NT/Probes/Match Probes with Specificity
14
15
16DESCRIPTION
17
18                Searches for potential probe target sites within the sequence
19                entries of the corresponding 'PT_SERVER' (not the current)
20                database from a list of named probes in a probe collection. Matching
21                is performed with the maximum allowable number of mismatches for
22                each given probe.
23
24                Probe collections are created or loaded with the PROBE COLLECTION
25                window. Probes must be named with unique names otherwise the
26                match results cannot be reconcilled correctly. Similarly, species
27                within the tree must also have unique names for the match processing
28                to work correctly.
29
30                To add a probe to the collection enter the 'Target String' and the
31                'Probe Name' and press the ADD button. To remove a probe from the
32                collection select the probe from the 'Probes' list and press the
33                REMOVE button. Pressing the 'FORGET' button will remove all probes
34                from the collection and start a fresh.
35
36                To save the probe collection to file press the 'SAVE' button and
37                to load a previously created collection press the 'LOAD' button.
38                Probe collections are stored in a simple XML format so they can
39                be easily created with an external text editor. The file format
40                is detailed below.
41
42                The 'Match Weighting' matrix specifies how mismatch penalities will
43                be alloted to sequence mismatches. The 'Positional Weighting'
44                parameters adjust the mismatch penalities according to position
45                through the following equations:
46
47                  S = -ln(10) / 'Width'
48
49                  P = (((2.0 * 'position') - 'length') / 'length') - 'Bias'
50
51                  Weight = exp(S * P * P)
52
53                where 'position' is the sequence position and 'length' is the probe
54                length. weighting function gives a bell curve shape whose spread
55                is controlled by the 'Width' parameter, centre is controlled
56                by the 'Bias' parameter and whose maximum is one.
57
58                For the default values of 1 and 0 for 'Width' and 'Bias' respectively
59                the weighting function has a value of 1 for a position that is half
60                the probe length and 0.1 at the zeroth position and the probe length
61                position.
62
63                The 'Match Weighting' and 'Positional Weighting' parameters are
64                saved as part of the probe collection XML file.
65
66                The MATCH PROBES WITH SPECIFICITY window is used to perform probe
67                collection matching. The 'Probes' list shows the probes in the
68                probe collection to be matched. If the list is empty you can click
69                on the EDIT button to open the PROBE COLLECTION window and create
70                or open a probe collection. The CLEAR button clears any previous
71                match results but leaves the probe collection in tact.
72
73                You need to select a 'PT_SERVER' from the menu displayed after
74                pressing the 'PT_SERVER' button before you can carry out a probe
75                collection match. Press the MATCH button to carry out the match
76                operation. When the match is complete the number of matches found
77                will be displayed and the complete list of match results can be
78                viewed by pressing the RESULTS button. Be warned that with large
79                probe collections this can be a very large text file.
80
81                Match results are displayed in the DENDROGRAM view using a series
82                of vertical bars (one bar per probe) on the left hand side indicating
83                regions in the tree where matches occur. Left mouse clicking on the
84                bar will open a status message telling you which probe the bar
85                corresponds to.
86
87SECTION         Match display control
88
89                What constitutes a match is controlled by the MATCH DISPLAY CONTROL
90                parameters in the MATCH DISPLAY CONTROL window. The controls
91                allow you to test, in real time, the match performance of probe
92                collections without having to re-run the time consuming match operation.
93
94                The 'Mismatch threshold' slider controls the threshold level that
95                dictates whether a partial match will be regarded as a match or a
96                mismatch. The scale of the 'Mismatch threshold' spans the range
97                from zero to the maximum match weight for the found match results.
98
99                The 'Clade marked threshold' slider controls the threshold level
100                (between 0 and 100%) that governs whether a clade is marked as
101                matched. For example, if the slider was set to 70% it would indicate
102                that at least 70% of species within a clade must match to the degree
103                dictated by the 'Mismatch threshold' before the clade is marked as
104                matched.
105
106                In a similar manner, the 'Clade partially marked threshold' slider
107                controls the threshold level (between 0 and 100%) that governs whether
108                a clade is marked as partially matched. Partial clade matches are
109                indicated with a stippled bar whereas for a full match the bar is
110                solid.
111
112                More options are available via 'Marker display settings'
113                (see LINK{nt_tree_marker_settings.hlp}).
114
115SECTION         Display interaction
116
117                  Click (and drag) on a marker shown in tree display, to
118                  display its name and to select the corresponding probe
119                  in the probe selection list.
120
121SECTION PROBE COLLECTION XML
122
123        <?xml version="1.0" encoding="UTF-8" standalone="no"?>
124        <!DOCTYPE probe_collection>
125        <probe_collection name="">
126            <probe_list>
127                <probe seq="AGGUCACACCCGUUCCCA" name="probe1"/>
128                <probe seq="AGGUCACACCCGUUCCCG" name="probe2"/>
129                <probe seq="AGGUCACACCCGUUCCCT" name="probe3"/>
130                    .
131                    .
132                    .
133            </probe_list>
134            <match_weighting width="1" bias="0">
135                <penalty_matrix values="0 1 1 2 1 0 1 1 1 1 0 1 2 1 1 0"/>
136            </match_weighting>
137        </probe_collection>
138
139
140        The penalty matrix values follow row major ordering.
141
142NOTES
143
144                The 'PT_SERVER' database ('*.arb' and '*.arb.pt') stored in
145                '$ARBHOME/lib/pts' is used for probe target searching not the
146                current database.
147
148                The 'PT_SERVER' database has to be updated ('ARB_NT/Probes/Probe
149                Admin') if species entries should be considered for probe target
150                searching which have been added or modified (sequence symbols)
151                later than the date of the most recent 'PT_SERVER' database
152                update.
153
154                Probe target searching does not depend on correctly aligned
155                sequences and is not affected by any modifications of database
156                entries except changes of sequence residues.
157
158
159EXAMPLES
160
161        None
162
163
164WARNINGS
165
166                Take care to ensure that all probes in the probe collection and all
167                species in the current database are uniquely named. Not doing so
168                will result in results not being displayed correctly.
169
170BUGS
171
172        No bugs known
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