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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