ARB is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.
ARB was primarily been developed for ribosomal ribonucleic acid (rRNA) sequences, and therefore contains special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures can be stored in the same database.
ARB is designed for a graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. The majority of operations can be controlled using the mouse for moving the pointer and the left mouse button for initiating and performing operations.
The following tools are available on ARB:
ARB_DB
- A central database of (aligned homologous) sequences and additional information, taken from public databases or supplied by the user, is stored in a (binary or ASCII) file (*.arb).
- The database can be structured according to phylogeny or other user-defined criteria.
- Tools for text-oriented database searching are integrated.
ARB_NT
- Phylogenetic trees derived from the data or imported from other sources are displayed within the main window. Different tree topologies, complete trees, and subtrees can be stored and used for walking through the database. Database entries can be shown with the tree on the screen or in separate windows. Trees can be used to define subsets of data for display or analysis by other ARB tools.
- Publication-ready trees can be produced by shaping the displayed tree topology and printing or exporting the tree to foreign software (TREETOOL [], XFIG []).
ARB_EDIT
An editor for the display of sequences and sequence-associated data (masks and filters, consensus sequences, higher-order structure) and basic editing functions is available. This tool allows manual entering of new sequences (with a customized keyboard, if desired); manual modification of alignments; search and replacement of sequence stretches; and printout of data. Predicted higher-order structure is automatically checked according to a user-provided mask, and may be displayed with the sequences by user-definable symbols.
ARB_ALIGN
The ARB tool for automated sequence alignment searches for the most similar sequences in the database and inserts the new sequence into an existing alignment according to primary and higher-order structural similarity.
ARB_IMPORT/EXPORT
ARB modules as well as integrated foreign software (GDE [1], READSEQ [2], CONVERTALIGN [3]) can be used for import and export of (subsets of) data in different formats, and for database merging.
ARB_PROTECTION
Up to six hierarchical protection levels can be individually asigned to database entries to prevent unintended modification or loss of data.
ARB_NAMES
Unique identifiers are automatically generated for the individual entries and stored with the database. This prevents multiple entries of the same data, and assignment of identical names to different data.
ARB_PHYL
ARB tools and integrated foreign software (PHYLIP [4], DE SOETE [1], fastDNAml [4]) allow calculation of similarity/distance matrices, conservation profiles, selection masks and phylogentic tree reconstruction using different treeing approaches.
ARB_PROBE
Species- and group-specific probes are designed and checked by searching the complete database for unique sequence stretches. Potential probe or target sites are ranked by user-supplied criteria for mismatch weighing.
An Example file can be found in this directory of your arb installation "/usr/software/sampledata/arb_demo_data"
A PDF manual can be found here http://www.arb-home.de
References:
Getting started notes [Pdf]
Design and Evaluation of 16S rRNA-Targeted Oligonucleotide Probes for Fluorescence In Situ Hybridization [Entrez]
ARB: a software environment for sequence data. Nucleic Acids Research 32(4):1363-1371. [Entrez]
Fluorescence in situ hybridization with rRNA-targeted oligonucleotide probes (PDF from J.Pernthaler, F.O.GlЖckner, W.SchЖnhuber, R.Amann) [Pdf]
|