Gene informationOCCURRENCE
ARB_GENEMAP/<INFO> button (on the left side)
ARB_NT/Genome/Gene information
ARB_NT/Genome/Search and Query/Info
ARB_GENEMAP/Genome/Gene information
ARB_GENEMAP/Genome/Search and Query/Info
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DESCRIPTION
Displays gene information stored within the 'fields' (see ´Glossary´).
The particular 'gene' (see ´Glossary´) can be 'marked' or 'unmarked' (see ´Glossary´) 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.
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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'
´Copy and Paste´ can be used in the 'Edit box' subwindow. This provides is easy way to manually export/import data.
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.
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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.
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NOTES
For gene-species 'codon_start' and 'transl_table' have the same meaning as described above.
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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
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