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Private Annotations

Alamut 2.1 introduces a new private annotations functionality. It enables the user to define manually and import automatically sequence based annotations, such as PCR Primers, probes, bibliography or memos.

This feature is available on a dedicated track.

To switch this feature on, check Display private annotations track in the Preferences panel (menu 'Tools' > 'Options').

Where and how private annotations are stored

As for variants, the basic annotation database functionality implementation relies on files stored either on each user's computer, or on a shared file system.
Private annotations are stored in local files, inside a folder that can be specified in the Preferences panel (menu 'Tools' > 'Options'). By default, this folder is 'AlamutFiles' (inside 'My Documents' on Windows XP or Windows 7, inside 'Documents' on Windows Vista, and inside the user's home folder on Mac and Linux):

Alamut creates individual annotation files per gene, named after the gene's official symbol and with extension 'apa' (e.g. MLH1.apa for MLH1 annotations and DMD.apa for DMD annotations; apa stands for Alamut Private Annotations).

Information As for variants, it is also possible to define a set of different folders for annotation files (menu 'Folders' > 'Annotations').
These folders can be used for different use cases or projects and the menu enables to easily switch from one folder to another:

When switching to another folder, the only visible annotations are those which are stored in a file within the selected folder, if any.
The first listed folder shortcut in the menu is always the one that has been defined in the Preferences panel (menu 'Tools' > 'Options', see above). Extra folder shortcuts can be added or removed from the menu.

Warning As for any important computer data, please backup annotation files regularly.
Warning When annotations are stored in a shared file system, caution must be taken so that 2 people don't edit concurrently annotations of the same gene.

Annotation files use a simple XML representation format, suitable for processing by other applications.

Creating and managing datasets

Private annotations are organized in sub-tracks called datasets.
Datasets are managed through the context menu (by right-clicking) of the 'Private Annotations' label:

Once created, each dataset is managed through the context menu (by right-clicking) of its own label:

Creating annotations

Create annotations from a nucleotide selection in the private annotations track and its associated context menu (by right-clicking inside the selection).

Private annotations are defined by a set of properties accessible in a dedicated editor:

Edit Comment

Once the annotation is saved, it is visible in its track and dataset:

Information Moving an annotation to another dataset (using the Dataset combo box) or to another genomic position (using From and To entry fields) is enabled in the annotation properties editor.

Importing annotations

Alamut supports the import of annotations in the BED and the BED detail formats.
It also supports the GFF version 2, the GFF version 3 and the GVF formats.

This facility enables to import files, manually (through the context menu, by right-clicking) or automatically (by checking Automatically import formatted files from folder in the Preferences panel), and to display data accordingly in additionnal tracks.


Information Importing requires files with appropriate extension (.bed, .gff, .gvf), to be placed in the appropriate folder.

Information It is possible to import BAM files from SAMtools, converted into BED, using the bamToBed utility of BEDTools.

Information Data available through a URL may also be imported by creating a Windows-like .url file. By default, data are supposed to be in the BED format and a dedicated field Type may be used to specify the appropriate format, see example. Once such a .url file is placed in a folder, Alamut behaves exactly as if the data were stored in a local file.

Warning BED files use 0-based coordinates: the first base of the chromosome is considered position 0.

Viewing annotations

Annotations are then displayed using the graphical features provided by these formats:

Simple BED annotations 
Complete BED annotations 
Detail BED annotations 
GFF3/GVF annotations 

Information Editing imported annotations is not possible.

Customizing imported annotations display

BED files

Alamut handles standard track lines within BED files: each track line defines a dataset which name is either the name or the description of the track line. Annotations following a track line are put in the named dataset. Track line variables taken into account are: name, description, type, color, useScore, itemRgb and url.

GFF3/GVF files

Customization of GFF3/GVF annotations files display relies on Alamut directives that have to be added ahead of such files (after the initial ##gff-version line). An Alamut directive is a single line starting with ##alamut: and followed by a set of conditions and instructions under the form feature=string separated by the ":" mark. Several Alamut directives can be put in such files.

Admissible conditions are source=string and/or type=string, where string is to be replaced by any value taken by the source field (column 2) or the type field (column 3) in the imported file.
A directive with no condition applies anyway.

Admissible instructions are either dataset=string, name=string, color=string, arrow=string, note=string and/or extLink=string, where string is to be replaced by source or type or by any tag of the attributes field (column 9) of the imported file.
When a directive applies, any instruction feature will be set to a value according to the provided string:
- if the string is source or type, the feature will be set to the value of the source field or of the type field in the imported file.
- if the string is any tag of the attributes field in the imported file, the feature will be set to the value associated to the tag.

Detailed example:

##gff-version 3

When type is "gene", dataset is set to "gene", name is set to the value of the "gene_name" tag and color is set to magenta.
When type is "transcript", dataset is set to "transcript", name is set to the value of the "transcript_name" tag and color is set to blue.
In other cases, dataset is set to type and name is set to type.
Other features are set to default as explained hereunder.

Information Default settings in directives:
- the default dataset is source. It can be set to type.
- the default name is Name. It can be set to any tag of the attributes field in the imported file.
- the default color is darkCyan. It can be set to a RGB string in decimal (R,G,B) or in hexa (#RGB).
- the default arrow is given by the strand field (column 7) of the imported file. It can be set to none, left, right or both.
- the default note (comment) is Note. It can be set to any tag of the attributes field in the imported file.
- the default extLink (external link) is automatically extracted from the attributes field when a value matches a web address. It can be set to any tag of the attributes field in the imported file.

Information The ":" character used to separate conditions and instructions may be replaced by some other punctuation marks (e.g. "+", "|" or "~" but not "#", "=" , ";" or ","), in case the ":" mark would be used elsewhere.

Information For each annotation, Alamut tries to apply sequentially directives of the file. The only first applicable directive is ever used.

Importing numerical annotations

Alamut also supports importing annotations as an histogram in a dedicated Numerical Annotations track.
To switch this utility on, check Display numerical annotations track in the Preferences panel (menu 'Tools' > 'Options').

Numerical annotations are managed through the context menu (by right-clicking) of the 'Numerical Annotations' label:

Once the file is imported manually, the histogram represents the number of times each genomic position is included in an annotation within the file.

Information Importing BED files in the numerical track has to be done manually.

Information Only a single BED file can be displayed in the numerical track at the same time.

© 2011 Interactive Biosoftware - Last modified: Dec 30, 2011