Alignment Annotator

Author: christoph.gille   Institut für Biochemie, Charité, Berlin
This page describes the user interface of the Alignment-Annotator server. The alignment view which is displayed in the black frame is explained in a separate manual .



Alignment Annotator annotates and renders sequence alignments. Features: The resulting HTML document is interactive and can either stand alone or be included in other web pages.
Annotated alignments can also be exported to text processors like MS-Word. This allows for further editing for example to create figures for publications.

Visualization does not require client side Java or plugins This service does not require Java.

Alignment Annotator Startpage

The start page has a resizable text area to enter sequences. All standard sequence and alignment formats and database references are supported. Try example by activating the check-box Sample data. The sequences can be specified in several different ways: Amino acid sequences and nucleotide sequences are supported. However, full functionality including annotations from services and 3D visualization is only available for amino acid sequences. Nucleotide sequences are assumed, if all sequences are composed of the letters A, C, T, G and N. Nevertheless, the molecule type can be set explicitly with the command set_molecule_type in the first script text.

Alignment computation

In most cases, server side alignment computation is performed with ClustalW. This is a rapid method and combinable with 3D-structure alignment. More acurate methods like T-Coffee can be selected with the script command use_aligner in the first script. Mixed sequence / 3D structure alignment can improve alignment quality of remote homologs and is conducted if structure data is loaded at the time of alignment computation. This is the case if 3D structure alignment is time consuming. By default, the program TM-align is used. It can only align pairs of structures. If more than two structures are provided, all n times (n-1) pair alignments are compiled by the server program. The advantage is that the result of each pair alignment can be stored in the cache and interrupted computations can be resumed. Structure alignment methods which natively align more than two structures often yield better results and can be selected with the script command use_aligner3D. Often, homologous 3D structures are available only for some of the sequences and structure alignment can be combined with the sequence based methods ClustalW and T-Coffee.

The result page

After submitting the data to the server, the rendered and interactive alignment will be shown in an embedded frame. It will look like:

It has its own server independent user interface for rapid modification of the alignment view and is described in the documentation of the alignment view. The order of sequences can be changed with the mouse, sequences and annotations can be dragged into the trash and the residue colors can be changed. These settings are persistently stored with the session. Other settings including checkboxes for wrapping long sequences or displaying secondary structure are not.

Conversely, the control elements above the alignment frame allow changes that require processing data on the server. For example annotation services can be selected, annotations can be typed manually and script commands can be added.

It may happen that the job prematurely terminates due to timeout. In this case, the job may still succeed if it is started again by reloading the page.


Manually defined annotations: Annotations can be defined explicitely using GFF-format. For example the following line will select residue 24 of the specified sequence:
seqNameOrNumber||Modified residue|24|24|.|.|.|Note=sample text
The color will be selected in the following way: There is a table which assigns a color to frequent feature names. If the name matches an entry in the table the respective color will be taken. Otherwise the default color is used. The color (RGB-hexadecimal, in the example green) can be overridden with the script command:
feature_colors Modified_residue=#00ff00 
Conversely, annotations can be defined with the script commands new_selection and add_annotation (See next section).
new_selection  24-24, seqNameOrNumber/Modified_residue
set_annotation Style=STYLE_UNDERLINE, seqNameOrNumber/Modified_residue
set_annotation Color=#00ff00, seqNameOrNumber/Modified_residue
add_annotation Balloon=pops up at the mouse pointer, seqNameOrNumber/Modified_residue
This is more verbose but allows to add various properties like 3D-styles. First capturing the name in a variable can reduce the size of the script text:
let $n=seqNameOrNumber/Modified_residue
Annotations from services: The UniProt sequence features and Catalytic Site Atlas residues are directly stored on the server and will be quickly available. The BioDAS services, however are loaded from remote servers which causes some delay. The default BioDAS services are cbs_total, netphos and netoglyc. All others are available with the script command DAS_features name, sequences. The selection of the color is described above.


Not all program features are accessible by the graphical user interface. Some advanced functionallity requires scripting.


The result can be downloaded as a zip file which contains all HTML files. It also contains examples showing, how alignments are embedded in web pages on web servers. There are no special requirements for the web server since all files are static. If 3D structures are associated to the sequences in the alignment, the respective PDB files and the applet software need to be copied into the same directory.

Embedding in web services

Alignment Annotator can dynamically visualize alignments for Bioinformatics web services. If you know a Bioinformatics software or database which should use Alignment Annotator visualization, please get in touch with the maintainer.

Developers find here the details of the programming interface.