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Last update on 04. Dec 2013 .
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SPECIES INFORMATION

OCCURRENCE

ARB_NT/<INFO> button: left area, fifth from top ARB_NT/Species/Info ARB_NT/Species/Search

 

DESCRIPTION

Displays species information stored within the 'fields' (see ´Glossary´).

The particular 'species' (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 sequences. 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 ENTRIES

The following database entries have a special meaning in ARB:

name            unique name for the species (generated by ARB)
full_name       full species name (generated by the user)
acc             Accession number (automatically generated by ARB if missing)

Entries 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, ...)

Commonly used database entries (e.g. by import/export):

entry           EMBL           Genebank

author          RA             REFERENCE/AUTHORS
title           RT             REFERENCE/TITLE
journal         RL             REFERENCE/JOURNAL
refgrp          RG             REFERENCE/CONSRTM
pubmed_id       RX PUBMED      REFERENCE/PUBMED
medline_id      RX MEDLINE     REFERENCE/PUBMED
version         SV             VERSION
keywd           KW             KEYWORDS
tax             OC             ORGANISM
comment         CC             COMMENT

description     DE
auth_comm       RC
nuc_rp          RP
db_xref         DR
date            DT
organelle       OG
definition                     DEFINITION

 

EXAMPLES

Update the 'full_name' 'Pseudomonas cepacia' to 'Comamonas
cepacia':
        Select FIELDS:  'full_name'
        Move cursor into the 'Edit box' subwindow
        Delete:         'Pseudomonas'
        Type:           'Comamonas'

 

WARNINGS

It is recommended to reset the protection level after modifying entries to prevent unintentional modification or loss of data.

 

BUGS

No bugs known