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Last update on 25. Nov 2018 .
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Gene information

OCCURRENCE

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

 

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.

 

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.

 

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