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#Please insert up references in the next lines (line starts with keyword UP)
UP arb.hlp
UP glossary.hlp
UP gene_search.hlp
UP Protection.hlp
#Please insert subtopic references (line starts with keyword SUB)
SUB spaf_reorder.hlp
SUB spaf_delete.hlp
SUB spaf_create.hlp
SUB scandb.hlp
SUB spa_delete.hlp
SUB spa_rename.hlp
SUB spa_copy.hlp
SUB gen_create.hlp
# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
#************* Title of helpfile !! and start of real helpfile ********
TITLE GENE INFORMATION
OCCURRENCE ARB_GENEMAP/<INFO> button (on the left side)
ARB_NT/Genes/Info
ARB_NT/Genes/Search
ARB_GENEMAP/Genes/Info
ARB_GENEMAP/Genes/Search
DESCRIPTION Displays gene information stored within the 'fields' (see LINK{glossary.hlp}).
The particular 'gene' (see LINK{glossary.hlp})
can be 'marked' or 'unmarked' (see LINK{glossary.hlp})
by pressing the checkbox after the 'Marked?' prompt.
Editing of 'field' entries is enabled or prevented by
pressing the 'Edit enabled?' checkbox.
The entries of a 'field' are modified by choosing it from
the 'DATABASE FIELDS' subwindow and modifying the entries
displayed in the 'Edit box' subwindow.
NOTES The 'SEARCH & QUERY' window can be displayed by pressing the <SEARCH>
button.
For modification of 'field' entries, a protection level
has to be selected from the Protection menu of the main
window (ARB_NT/Protection) equal to or higher than that
assigned to the selected 'field'
Cut and paste of the window system can be used in the 'Edit
box' subwindow. This provides is an easy way to export/import
data.
Use the left mouse button to mark (cut is done automatically).
Then use the middle mouse button to paste.
When you open this window it will always show the information of
the current species. That means if you select another species (in ARB_NT or in the editor)
this window will follow and display information of the selected species.
After clicking on the <DETACH> button once the window will no longer follow the current
species automatically. You may open a new information window then (which will follow again).
Clicking again on the <DETACH> button will catch up the detached window to the current species.
SECTION STANDARD FIELDS
The following fields have a special meaning in ARB:
name unique identifier for the gene/annotation
(should be max. 8 characters long; generated by ARB)
type type of gene
(e.g. 'gene', 'CDS', 'tRNA', 'misc_feature', ...)
pos_start start position(s) of gene; range is 1..genomeLength
pos_stop stop position(s) of gene; range is 1..genomeLength
pos_complement 1 -> gene is located on other strand
pos_certain contains information about the certainty of start and
stop position(s):
- 1st character refers to start-position,
- 2nd to stop-position.
Possible characters:
'=' means 'pos is exact'
'<' means 'pos may be lower'
'>' means 'pos may be higher'
'+' means 'pos is directly behind'
'-' means 'pos is directly before'
If the entry is missing, it is assumed that all positions are exact.
pos_joined contains the number of parts a joined gene consist of.
>0 parts maybe joined (location 'join(...)').
<0 it's unknown whether parts a joinable (location 'order(...)').
if the field is missing, 1 is assumed (which means "simple gene"; e.g. "205..377")
if pos_joined contains a value diff from '1', the fields 'pos_start' to
'pos_certain' each contains a semicolon-separated-list of what's described above.
The list contains one element for each part.
ARB_display_hidden gene will not be displayed
(and is not found by default with search tool)
Use the Hide-menu in ARB_GENEMAP to modify the hidden-status.
Note: the importer automatically hides all genes with type 'gene', if
another entry with different type exists at the same location.
ARB_is_gene ID ('name') of gene (with type 'gene')
at same location
During import ARB removes all 'translation' qualifiers from the feature
table, if it can reproduce them.
ARB_translation if 'translation' was NOT reproducible, this
contains the result of the translation. In
this case the 'translation' has not been removed by ARB.
ARB_translation_note additional information about reproduction
ARB_translation_rm 1 -> ARB has reproduced+removed the translation
Fields relevant for DNA->AminoAcid encoding:
codon_start contains the base inside the gene at which the
first codon starts (valid: 1,2,3)
if this entry is missing 1 is assumed
transl_table the number of the translation table to be used
(1 = Standard, ...). Same table numbers as used by EMBL.
NOTES For gene-species 'codon_start' and 'transl_table' have the same
meaning as described above.
WARNINGS It is recommended to reset the protection level after
modifying entries to prevent unintentional modification
or loss of data.
The genom flat file format often contains the entries 'codon_start' and 'transl_table'
inside the sub-entry CDS (CDS_01,...).
Use Search&Query + Mark to fields of listed species to correct this
BUGS No bugs known
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