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Last update on 25. Nov 2018 .
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SPECIES INFORMATION

OCCURRENCE

ARB_NT/<INFO> button (top area; showing the short name of the selected species)

ARB_NT/Species/Species Information

ARB_NT/Species/Search/Info button

ARB_NT/Info mode button (in the button bar on the left side)

ARB_EDIT4/Info mode button

ARB_PARSIMONY/Info mode button

 

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'

´Copy and Paste´ can be used in the 'Edit box' subwindow. This provides is easy way to manually export/import (sequence) data.

 

Locking information window to a specific species

When you open this window it will always show the information of the currently ´Selected species´. That means if you select another species (in the tree or in the editor) this window will follow your selection and display the information of the newly selected species.

By pressing the 'Lock view' button you will open a second information window which will be LOCKED TO the currently selected species. That second information window will NOT FOLLOW the selected species (as the primary information window does). Instead of the 'Lock view' button, it shows an 'Update' button. Pressing the 'Update' button will change the displayed species to the species currently selected.

You can distinguish the two types of information windows by their window title and by the color of the area showing the ID of the selected species.

 

STANDARD ENTRIES

The following database entries have a special meaning in ARB:

name            unique species ID (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