source: branches/lib/HELP_SOURCE/source/gene_info.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: 6.7 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      gene_search.hlp
5UP      Protection.hlp
6
7#       sub topics:
8SUB     spaf_reorder.hlp
9SUB     spaf_delete.hlp
10SUB     spaf_create.hlp
11SUB     scandb.hlp
12SUB     spa_delete.hlp
13SUB     spa_rename.hlp
14SUB     spa_copy.hlp
15SUB     gen_create.hlp
16
17# format described in ../help.readme
18
19
20TITLE           Gene information
21
22OCCURRENCE      ARB_GENEMAP/<INFO> button (on the left side)
23                ARB_NT/Genome/Gene information
24                ARB_NT/Genome/Search and Query/Info
25                ARB_GENEMAP/Genome/Gene information
26                ARB_GENEMAP/Genome/Search and Query/Info
27
28DESCRIPTION     Displays gene information stored within the 'fields' (see LINK{glossary.hlp}).
29
30                The particular 'gene' (see LINK{glossary.hlp})
31                can be 'marked' or 'unmarked' (see LINK{glossary.hlp})
32                by pressing the checkbox after the 'Marked?' prompt.
33
34                Editing of 'field' entries is enabled or prevented by
35                pressing the 'Edit enabled?' checkbox.
36
37                The entries of a 'field' are modified by choosing it from
38                the 'DATABASE FIELDS' subwindow and modifying the entries
39                displayed in the 'Edit box' subwindow.
40
41NOTES           The 'SEARCH & QUERY' window can be displayed by pressing the <SEARCH>
42                button.
43
44                For modification of 'field' entries, a protection level
45                has to be selected from the Protection menu of the main
46                window (ARB_NT/Protection) equal to or higher than that
47                assigned to the selected 'field'
48
49                LINK{copyNpaste.hlp} can be used in the 'Edit box' subwindow.
50                This provides is easy way to manually export/import data.
51
52                When you open this window it will always show the information of
53                the current species. That means if you select another species (in ARB_NT or in the editor)
54                this window will follow and display information of the selected species.
55                After clicking on the <DETACH> button once the window will no longer follow the current
56                species automatically. You may open a new information window then (which will follow again).
57                Clicking again on the <DETACH> button will catch up the detached window to the current species.
58
59SECTION         STANDARD FIELDS
60
61                The following fields have a special meaning in ARB:
62
63                    name            unique identifier for the gene/annotation
64                                    (should be max. 8 characters long; generated by ARB)
65                    type            type of gene
66                                    (e.g. 'gene', 'CDS', 'tRNA', 'misc_feature', ...)
67                    pos_start       start position(s) of gene; range is 1..genomeLength
68                    pos_stop        stop position(s) of gene; range is 1..genomeLength
69                    pos_complement  1 -> gene is located on other strand
70                    pos_certain     contains information about the certainty of start and
71                                    stop position(s):
72
73                                    - 1st character refers to start-position,
74                                    - 2nd to stop-position.
75
76                                    Possible characters:
77
78                                    '='       means 'pos is exact'
79                                    '<'       means 'pos may be lower'
80                                    '>'       means 'pos may be higher'
81                                    '+'       means 'pos is directly behind'
82                                    '-'       means 'pos is directly before'
83
84                                    If the entry is missing, it is assumed that all positions are exact.
85
86                    pos_joined      contains the number of parts a joined gene consist of.
87
88                                    >0   parts maybe joined (location 'join(...)').
89                                    <0   it's unknown whether parts a joinable (location 'order(...)').
90
91                                    if the field is missing, 1 is assumed (which means "simple gene"; e.g. "205..377")
92
93                                    if pos_joined contains a value diff from '1', the fields 'pos_start' to
94                                    'pos_certain' each contains a semicolon-separated-list of what's described above.
95                                    The list contains one element for each part.
96
97
98                    ARB_display_hidden       gene will not be displayed
99                                             (and is not found by default with search tool)
100
101                                             Use the Hide-menu in ARB_GENEMAP to modify the hidden-status.
102                                             Note: the importer automatically hides all genes with type 'gene', if
103                                                   another entry with different type exists at the same location.
104
105                    ARB_is_gene              ID ('name') of gene (with type 'gene')
106                                             at same location
107
108                During import ARB removes all 'translation' qualifiers from the feature
109                table, if it can reproduce them.
110
111                    ARB_translation          if 'translation' was NOT reproducible, this
112                                             contains the result of the translation. In
113                                             this case the 'translation' has not been removed by ARB.
114                    ARB_translation_note     additional information about reproduction
115                    ARB_translation_rm       1 -> ARB has reproduced+removed the translation
116
117                Fields relevant for DNA->AminoAcid encoding:
118
119                    codon_start     contains the base inside the gene at which the
120                                    first codon starts (valid: 1,2,3)
121                                    if this entry is missing 1 is assumed
122                    transl_table    the number of the translation table to be used
123                                    (1 = Standard, ...). Same table numbers as used by EMBL.
124
125NOTES           For gene-species 'codon_start' and 'transl_table' have the same
126                meaning as described above.
127
128WARNINGS        It is recommended to reset the protection level after
129                modifying entries to prevent unintentional modification
130                or loss of data.
131
132                The genom flat file format often contains the entries 'codon_start' and 'transl_table'
133                inside the sub-entry CDS (CDS_01,...).
134                Use Search&Query + Mark to fields of listed species to correct this
135
136BUGS            No bugs known
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