source: branches/lib/HELP_SOURCE/source/probematch.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 4.2 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      pt_server.hlp
5
6#       sub topics:
7#SUB     subtopic.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Probe Match
13
14OCCURRENCE      ARB_NT/Probes/Match Probes
15
16DESCRIPTION     Finds and displays all occurrences of a given target and/or
17                probe sequence within any specified 'PT_SERVER' database. The
18                species, targets and additional information are ranked and
19                displayed according to the degree of similarity.
20
21                Select a 'PT_SERVER' from the menu displayed after
22                pressing the 'PT_SERVER' button of the 'PROBE MATCH'
23                window.
24
25                Define whether similar (not perfectly matched) sites
26                should be displayed by pressing the 'Search depth'
27                button and selecting the number of mismatches (1 - 20)
28                from the menu.
29
30                Check the 'Use weighted mismatches' switch to use the
31                custom weights defined via 'EXPERT' button (see LINK{pm_spec_param.hlp}).
32
33                Define whether the species which contain the target or
34                probe (or similar) sequence should be marked (see
35                LINK{mark.hlp}) by enabling the 'Mark in database'
36                toggle.
37
38                Define if probe AND target sequence should be searched
39                by enabling the 'Check rev.compl. too' toggle.
40
41                Press the 'MATCH' button to perform the search.
42
43                Enabling the 'Auto (match)' toggle will automatically
44                start a probe match whenever the target string is
45                changed. Try it when you design probes.
46
47                The results will be displayed within the display area,
48                ranked according to the degree of similarity between
49                probe string and database entries.
50
51                Brief description of the listed columns:
52
53                  - name: ID (shortname) of matched species
54                  - fullname: full name of the matched species
55                  - mis: number of mismatches
56                  - N_mis: number of pairings with ambiguous residues (N)
57                  - wmis: mismatch weights
58                  - pos: alignment position of match
59                  - rev: 0=normal match; 1=reverse complement match
60
61                Results from gene PT_servers consist of different columns:
62
63                  - organism: ID (shortname) of matched organism
64                  - genename: ID (shortname) of matched gene
65                  - mis, N_mis, wmis, rev (same meaning as with normal PT_server)
66                  - pos: position of match in genome sequence
67                  - gpos: position of match in gene sequence
68
69                Sequence sections containing stretches identical or
70                similar to the probe string or its reversed complement
71                are shown between dashes in the last column:
72
73                    Perfectly matched positions are indicated by
74                    double dashes, mismatches by base symbols.  The
75                    (hybrid destabilizing) quality of mismatches is
76                    indicated by upper and lower case letters.
77
78#               To write the results to an ascii file press the 'SAVE'
79#               button to display the 'SELECTION BOX' window.
80
81                The 'IUPAC' button allows to match multiple probes
82                by specifying a probe containing IUPAC codes (see LINK{pd_match_iupac.hlp}).
83
84NOTES           Unlike the 'ARB_PROBE_DESIGN' tool, the 'ARB_PROBE_MATCH' tool
85                does not depend on the consistency of the current and the
86                'PT_SERVER' database. Any 'PT_SERVER' database containing
87                homologous or non-homologous, aligned or crude data can be
88                searched for potential probe target matches.
89
90                Please note that all positions returned from PT-Server are in
91                the range [0..N-1]. They differ by 1 from positions in ARB_EDIT4.
92
93                See LINK{copyNpaste.hlp} for howto paste text into the probe target field.
94
95EXAMPLES        None
96
97WARNINGS        None
98
99BUGS            The number of results is limited to 1000000 hits by default.
100                You may change that limit in the expert subwindow.
101
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