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More documentation can be found on the ARB website.
Last update on 08. Apr 2009 .
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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 ´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 name for the gene/annotation
                (max 8 characters long; generated by ARB)
pos_begin       start position of the gene in the main-sequence
                of the organism.
pos_end         end position of the gene
                Note: pos_begin <= pos_end
                      positions go from 1 to N
pos_uncertain   if either pos_begin or pos_end is uncertain
                this field contains a string build from <,>,=
                The first character of the field corresponds
                to pos_begin, the second character to pos_end.
                < means the position may be lower
                > -----------"------------- higher
                = means: the position is certain
pos_joined      If this field exists, it contains a number X>1
                In this case the gene is joined from X parts
                and it contains further fields pos_begin2,
                pos_begin3, ... (up to pos_beginX) containing
                the start positions of the other parts. The
                same applies to the fields pos_end and
                pos_uncertain.
complement      if complement is 1, the coding direction of
                the gene is from right to left.
                        

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, ...)
                        

 

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