flexible tool to search allen brain atlases

View the Project on GitHub fredpdavis/allenminer

ALLENMINER - a tool for identification of genes expressed in patterns of interested using the Allen Brain Atlas.

v2.1; 2015 Dec 10


ALLENMINER searches for genes that express in patterns of interest in the developing or adult mouse Allen Brain Atlases (ABA).

It can search in any region of interest for genes that: 1. express 2. express specifically 3. express non-uniformly 4. express in a graded fashion 5. express in a pattern similar to a query gene

The region of interest can be specified as a set of brain region names or as x,y,z bounds of a cuboid region of interest.

The code includes several routines that are generally useful for processing ABA data files, including parsers for XML and XPZ files. Besides accessing the raw data, these routines are useful for visualizing ABA expression files on platforms where the ABA BrainExplorer application is not available (eg, GNU/Linux). For example, all ABA expression files can be converted to PDB (protein data bank) format for visualization in protein structure viewers, such as PyMOL (

For more details take a look at the users manual.

What's new in v2.1? (2015 Dec 10)

Version 2.1 is compatible with the latest adult (v7) and developing (v6) brain atlases.

External Software

The program requires four programs, usually installed on most machines: Perl, wget, unzip, and gzip. Mac OS/X machines may not have wget by default, so check and download if necessary. PyMol or other PDB viewers are useful to visualize ROI partition definitions when performing a graded or patterning query.


A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas. F. P. Davis and S. R. Eddy. Bioinformatics 2009.