| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | UP pt_server.hlp |
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| 5 | |
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| 6 | #Please insert subtopic references (line starts with keyword SUB) |
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| 7 | #SUB sub.hlp |
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| 8 | |
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| 9 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 10 | |
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| 11 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 12 | TITLE Probe Match |
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| 13 | |
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| 14 | OCCURRENCE ARB_NT/Probes/Match Probes |
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| 15 | |
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| 16 | DESCRIPTION Finds and displays all occurrences of a given target and/or |
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| 17 | probe sequence within any specified 'PT_SERVER' database. The |
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| 18 | species, targets and additional information are ranked and |
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| 19 | displayed according to the degree of similarity. |
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| 20 | |
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| 21 | Select a 'PT_SERVER' from the menu displayed after |
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| 22 | pressing the 'PT_SERVER' button of the 'PROBE MATCH' |
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| 23 | window. |
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| 24 | |
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| 25 | Define whether similar (not perfectly matched) sites |
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| 26 | should be displayed by pressing the 'Search depth' |
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| 27 | button and selecting the number of mismatches (1 - 20) |
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| 28 | from the menu. |
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| 29 | |
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| 30 | Check the 'Use weighted mismatches' switch to use the |
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| 31 | custom weights defined via 'EXPERT' button (see LINK{pm_spec_param.hlp}). |
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| 32 | |
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| 33 | Define whether the species which contain the target or |
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| 34 | probe (or similar) sequence should be marked (see |
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| 35 | LINK{mark.hlp}) by enabling the 'Mark in database' |
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| 36 | toggle. |
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| 37 | |
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| 38 | Define if probe AND target sequence should be searched |
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| 39 | by enabling the 'Check rev.compl. too' toggle. |
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| 40 | |
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| 41 | Press the 'MATCH' button to perform the search. |
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| 42 | |
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| 43 | Enabling the 'Auto (match)' toggle will automatically |
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| 44 | start a probe match whenever the target string is |
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| 45 | changed. Try it when you design probes. |
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| 46 | |
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| 47 | The results will be displayed within the display area, |
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| 48 | ranked according to the degree of similarity between |
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| 49 | probe string and database entries. |
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| 50 | |
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| 51 | Brief description of the listed columns: |
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| 52 | |
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| 53 | - name: ID (shortname) of matched species |
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| 54 | - fullname: full name of the matched species |
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| 55 | - mis: number of mismatches |
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| 56 | - N_mis: number of pairings with ambiguous residues (N) |
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| 57 | - wmis: mismatch weights |
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| 58 | - pos: alignment position of match |
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| 59 | - rev: 0=normal match; 1=reverse complement match |
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| 60 | |
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| 61 | Results from gene PT_servers consist of different columns: |
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| 62 | |
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| 63 | - organism: ID (shortname) of matched organism |
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| 64 | - genename: ID (shortname) of matched gene |
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| 65 | - mis, N_mis, wmis, rev (same meaning as with normal PT_server) |
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| 66 | - pos: position of match in genome sequence |
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| 67 | - gpos: position of match in gene sequence |
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| 68 | |
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| 69 | Sequence sections containing stretches identical or |
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| 70 | similar to the probe string or its reversed complement |
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| 71 | are shown between dashes in the last column: |
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| 72 | |
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| 73 | Perfectly matched positions are indicated by |
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| 74 | double dashes, mismatches by base symbols. The |
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| 75 | (hybrid destabilizing) quality of mismatches is |
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| 76 | indicated by upper and lower case letters. |
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| 77 | |
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| 78 | # To write the results to an ascii file press the 'SAVE' |
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| 79 | # button to display the 'SELECTION BOX' window. |
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| 80 | |
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| 81 | The 'IUPAC' button allows to match multiple probes |
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| 82 | by specifying a probe containing IUPAC codes (see LINK{pd_match_iupac.hlp}). |
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| 83 | |
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| 84 | NOTES Unlike the 'ARB_PROBE_DESIGN' tool, the 'ARB_PROBE_MATCH' tool |
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| 85 | does not depend on the consistency of the current and the |
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| 86 | 'PT_SERVER' database. Any 'PT_SERVER' database containing |
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| 87 | homologous or non-homologous, aligned or crude data can be |
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| 88 | searched for potential probe target matches. |
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| 89 | |
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| 90 | Please note that all positions returned from PT-Server are in |
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| 91 | the range [0..N-1]. They differ by 1 from positions in ARB_EDIT4. |
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| 92 | |
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| 93 | See LINK{copyNpaste.hlp} for howto paste text into the probe target field. |
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| 94 | |
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| 95 | EXAMPLES None |
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| 96 | |
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| 97 | WARNINGS None |
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| 98 | |
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| 99 | BUGS The number of results is limited to 1000000 hits by default. |
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| 100 | You may change that limit in the expert subwindow. |
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| 101 | |
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