| 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 gene_search.hlp |
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| 5 | UP Protection.hlp |
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| 6 | |
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| 7 | #Please insert subtopic references (line starts with keyword SUB) |
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| 8 | SUB spaf_reorder.hlp |
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| 9 | SUB spaf_delete.hlp |
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| 10 | SUB spaf_create.hlp |
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| 11 | SUB scandb.hlp |
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| 12 | SUB spa_delete.hlp |
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| 13 | SUB spa_rename.hlp |
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| 14 | SUB spa_copy.hlp |
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| 15 | SUB gen_create.hlp |
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| 16 | |
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| 17 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 18 | |
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| 19 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 20 | TITLE Gene information |
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| 21 | |
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| 22 | OCCURRENCE ARB_GENEMAP/<INFO> button (on the left side) |
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| 23 | ARB_NT/Genome/Gene information |
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| 24 | ARB_NT/Genome/Search and Query/Info |
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| 25 | ARB_GENEMAP/Genome/Gene information |
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| 26 | ARB_GENEMAP/Genome/Search and Query/Info |
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| 27 | |
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| 28 | DESCRIPTION Displays gene information stored within the 'fields' (see LINK{glossary.hlp}). |
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| 29 | |
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| 30 | The particular 'gene' (see LINK{glossary.hlp}) |
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| 31 | can be 'marked' or 'unmarked' (see LINK{glossary.hlp}) |
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| 32 | by pressing the checkbox after the 'Marked?' prompt. |
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| 33 | |
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| 34 | Editing of 'field' entries is enabled or prevented by |
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| 35 | pressing the 'Edit enabled?' checkbox. |
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| 36 | |
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| 37 | The entries of a 'field' are modified by choosing it from |
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| 38 | the 'DATABASE FIELDS' subwindow and modifying the entries |
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| 39 | displayed in the 'Edit box' subwindow. |
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| 40 | |
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| 41 | NOTES The 'SEARCH & QUERY' window can be displayed by pressing the <SEARCH> |
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| 42 | button. |
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| 43 | |
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| 44 | For modification of 'field' entries, a protection level |
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| 45 | has to be selected from the Protection menu of the main |
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| 46 | window (ARB_NT/Protection) equal to or higher than that |
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| 47 | assigned to the selected 'field' |
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| 48 | |
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| 49 | LINK{copyNpaste.hlp} can be used in the 'Edit box' subwindow. |
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| 50 | This provides is easy way to manually export/import data. |
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| 51 | |
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| 52 | When you open this window it will always show the information of |
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| 53 | the current species. That means if you select another species (in ARB_NT or in the editor) |
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| 54 | this window will follow and display information of the selected species. |
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| 55 | After clicking on the <DETACH> button once the window will no longer follow the current |
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| 56 | species automatically. You may open a new information window then (which will follow again). |
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| 57 | Clicking again on the <DETACH> button will catch up the detached window to the current species. |
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| 58 | |
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| 59 | SECTION STANDARD FIELDS |
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| 60 | |
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| 61 | The following fields have a special meaning in ARB: |
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| 62 | |
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| 63 | name unique identifier for the gene/annotation |
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| 64 | (should be max. 8 characters long; generated by ARB) |
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| 65 | type type of gene |
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| 66 | (e.g. 'gene', 'CDS', 'tRNA', 'misc_feature', ...) |
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| 67 | pos_start start position(s) of gene; range is 1..genomeLength |
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| 68 | pos_stop stop position(s) of gene; range is 1..genomeLength |
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| 69 | pos_complement 1 -> gene is located on other strand |
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| 70 | pos_certain contains information about the certainty of start and |
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| 71 | stop position(s): |
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| 72 | |
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| 73 | - 1st character refers to start-position, |
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| 74 | - 2nd to stop-position. |
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| 75 | |
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| 76 | Possible characters: |
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| 77 | |
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| 78 | '=' means 'pos is exact' |
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| 79 | '<' means 'pos may be lower' |
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| 80 | '>' means 'pos may be higher' |
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| 81 | '+' means 'pos is directly behind' |
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| 82 | '-' means 'pos is directly before' |
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| 83 | |
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| 84 | If the entry is missing, it is assumed that all positions are exact. |
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| 85 | |
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| 86 | pos_joined contains the number of parts a joined gene consist of. |
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| 87 | |
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| 88 | >0 parts maybe joined (location 'join(...)'). |
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| 89 | <0 it's unknown whether parts a joinable (location 'order(...)'). |
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| 90 | |
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| 91 | if the field is missing, 1 is assumed (which means "simple gene"; e.g. "205..377") |
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| 92 | |
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| 93 | if pos_joined contains a value diff from '1', the fields 'pos_start' to |
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| 94 | 'pos_certain' each contains a semicolon-separated-list of what's described above. |
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| 95 | The list contains one element for each part. |
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| 96 | |
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| 97 | |
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| 98 | ARB_display_hidden gene will not be displayed |
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| 99 | (and is not found by default with search tool) |
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| 100 | |
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| 101 | Use the Hide-menu in ARB_GENEMAP to modify the hidden-status. |
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| 102 | Note: the importer automatically hides all genes with type 'gene', if |
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| 103 | another entry with different type exists at the same location. |
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| 104 | |
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| 105 | ARB_is_gene ID ('name') of gene (with type 'gene') |
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| 106 | at same location |
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| 107 | |
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| 108 | During import ARB removes all 'translation' qualifiers from the feature |
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| 109 | table, if it can reproduce them. |
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| 110 | |
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| 111 | ARB_translation if 'translation' was NOT reproducible, this |
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| 112 | contains the result of the translation. In |
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| 113 | this case the 'translation' has not been removed by ARB. |
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| 114 | ARB_translation_note additional information about reproduction |
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| 115 | ARB_translation_rm 1 -> ARB has reproduced+removed the translation |
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| 116 | |
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| 117 | Fields relevant for DNA->AminoAcid encoding: |
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| 118 | |
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| 119 | codon_start contains the base inside the gene at which the |
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| 120 | first codon starts (valid: 1,2,3) |
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| 121 | if this entry is missing 1 is assumed |
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| 122 | transl_table the number of the translation table to be used |
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| 123 | (1 = Standard, ...). Same table numbers as used by EMBL. |
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| 124 | |
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| 125 | NOTES For gene-species 'codon_start' and 'transl_table' have the same |
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| 126 | meaning as described above. |
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| 127 | |
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| 128 | WARNINGS It is recommended to reset the protection level after |
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| 129 | modifying entries to prevent unintentional modification |
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| 130 | or loss of data. |
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| 131 | |
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| 132 | The genom flat file format often contains the entries 'codon_start' and 'transl_table' |
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| 133 | inside the sub-entry CDS (CDS_01,...). |
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| 134 | Use Search&Query + Mark to fields of listed species to correct this |
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| 135 | |
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| 136 | BUGS No bugs known |
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