source: tags/arb_5.1/HELP_SOURCE/oldhelp/gene_info.hlp

Last change on this file was 6142, checked in by westram, 15 years ago
  • backport [6141] (parts not affecting code at all, i.e. helpfiles, figs, ..)
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 6.5 KB
Line 
1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      gene_search.hlp
5UP  Protection.hlp
6
7#Please insert subtopic references  (line starts with keyword SUB)
8SUB     spaf_reorder.hlp
9SUB     spaf_delete.hlp
10SUB     spaf_create.hlp
11SUB     spaf_scandb.hlp
12SUB     spa_delete.hlp
13SUB     spa_rename.hlp
14SUB     spa_copy.hlp
15SUB     spa_create.hlp
16
17# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
18
19#************* Title of helpfile !! and start of real helpfile ********
20TITLE           GENE INFORMATION
21
22OCCURRENCE      ARB_GENEMAP/<INFO> button (on the left side)
23                ARB_NT/Genes/Info
24                ARB_NT/Genes/Search
25                ARB_GENEMAP/Genes/Info
26                ARB_GENEMAP/Genes/Search
27
28DESCRIPTION     Displays gene information stored within the 'fields' (see LINK{glossary.hlp}).
29                The particular 'gene' (see LINK{glossary.hlp})
30                can be 'marked' or 'unmarked' (see LINK{glossary.hlp})
31                by pressing the checkbox after the 'Marked?' prompt.
32                Editing of 'field' entries is enabled or prevented by
33                pressing the 'Edit enabled?' checkbox.
34
35                The entries of a 'field' are modified by choosing it from
36                the 'DATABASE FIELDS' subwindow and modifying the entries
37                displayed in the 'Edit box' subwindow.
38
39NOTES           The 'SEARCH & QUERY' window can be displayed by pressing the <SEARCH>
40                button.
41
42                For modification of 'field' entries, a protection level
43                has to be selected from the Protection menu of the main
44                window (ARB_NT/Protection) equal to or higher than that
45                assigned to the selected 'field'
46
47                Cut and paste of the window system can be used in the 'Edit
48                box' subwindow. This provides is an easy way to export/import
49                data.
50                Use the left mouse button to mark (cut is done automatically).
51                Then use the middle mouse button to paste.
52
53                When you open this window it will always show the information of
54                the current species. That means if you select another species (in ARB_NT or in the editor)
55                this window will follow and display information of the selected species.
56                After clicking on the <DETACH> button once the window will no longer follow the current
57                species automatically. You may open a new information window then (which will follow again).
58                Clicking again on the <DETACH> button will catch up the detached window to the current species.
59
60SECTION         STANDARD FIELDS
61
62                The following fields have a special meaning in ARB:
63
64                name            unique name for the gene/annotation
65                                (should be max. 8 characters long; generated by ARB)
66                type            type of gene
67                                (e.g. 'gene', 'CDS', 'tRNA', 'misc_feature', ...)
68                pos_start       start position(s) of gene; range is 1..genomeLength
69                pos_stop        stop position(s) of gene; range is 1..genomeLength
70                pos_complement  1 -> gene is located on other strand
71                pos_certain     contains information about the certainty of start and
72                                stop position(s):
73
74                                - 1st character refers to start-position,
75                                - 2nd to stop-position.
76
77                                Possible characters:
78
79                                '='       means 'pos is exact'         
80                                '<'       means 'pos may be lower'     
81                                '>'       means 'pos may be higher'     
82                                '+'       means 'pos is directly behind'
83                                '-'       means 'pos is directly before'
84
85                                If the entry is missing, it is assumed that all positions are exact.
86
87                pos_joined      contains the number of parts a joined gene consist of.
88
89                                >0   parts maybe joined (location 'join(...)').
90                                <0   it's unknown whether parts a joinable (location 'order(...)').
91
92                                if the field is missing, 1 is assumed (which means "simple gene"; e.g. "205..377")
93
94                                if pos_joined contains a value diff from '1', the fields 'pos_start' to
95                                'pos_certain' each contains a semicolon-separated-list of what's described above.
96                                The list contains one element for each part.
97
98
99                ARB_display_hidden       gene will not be displayed
100                                         (and is not found by default with search tool)
101
102                                         Use the Hide-menu in ARB_GENEMAP to modify the hidden-status.
103                                         Note: the importer automatically hides all genes with type 'gene', if
104                                               another entry with different type exists at the same location.
105
106                ARB_is_gene              shortname of gene (with type 'gene')
107                                         at same location
108
109                During import ARB removes all 'translation' qualifiers from the feature
110                table, if it can reproduce them.
111
112                ARB_translation          if 'translation' was NOT reproducible, this
113                                         contains the result of the translation. In
114                                         this case the 'translation' has not been removed by ARB.
115                ARB_translation_note     additional information about reproduction
116                ARB_translation_rm       1 -> ARB has reproduced+removed the translation
117               
118                Fields relevant for DNA->AminoAcid encoding:
119
120                codon_start     contains the base inside the gene at which the
121                                first codon starts (valid: 1,2,3)
122                                if this entry is missing 1 is assumed
123                transl_table    the number of the translation table to be used
124                                (1 = Standard, ...). Same table numbers as used by EMBL.
125
126NOTES           For gene-species 'codon_start' and 'transl_table' have the same
127                meaning as described above
128
129WARNINGS        It is recommended to reset the protection level after
130                modifying entries to prevent unintentional modification
131                or loss of data.
132
133                The genom flat file format often contains the entries 'codon_start' and 'transl_table'
134                inside the sub-entry CDS (CDS_01,...).
135                Use Search&Query + Mark to fields of listed species to correct this
136
137BUGS            No bugs known
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