| More docs on the ARB website. See also index of helppages. Last update on 27. Jun 2017 .

Main topics:

- ARB: a Short Introduction
- Glossary
- Search Database for Genes
- Set protection level

Related topics:

- Reorder Fields
- Delete Fields
- Create a Field
- Scan Database for all Fields
- Delete Species/Gene
- Rename Species/Gene
- Copy Species/Gene
- Create Gene / Edit location

# GENE INFORMATION

- OCCURRENCE
- DESCRIPTION
- NOTES
- STANDARD FIELDS
- NOTES
- WARNINGS
- BUGS

## 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 ´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'

### 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.

## 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