Welcome to SOLVE-Brain

SOLVE-Brain version 1.0.3 release! New features include:

  • 1) Web interface now available using HTML5 sessionStorage.

  • 2) Updated version of DBDB genes

Please see our tutorial for updates.


This is a tissue-specific annotation tools for gene discovery experiments using next-generation sequencing data. In this case, it's focused on finding brain-specific genes.

If you have a variant call file with basic annotations from Annovar, this tool is for you. Probably you want to know whether any of the variants in that file are especially interesting. If you are like us, you may want to know if any of those variants are causative of a developmental brain phenotype. This is often where the programmatic evaluation of candidate genes breaks down, and many a talented bioinformatician is left at this stage manually "looking things up." That's a hassle. We got tired of manually looking things up. So we built SOLVE-Brain to make life a little bit easier, a little bit faster.


1) Handles multi-sample vcfs and sorts for you by pedigree hypothesis (i.e. de novo, autosomal dominant, autosomal recessive, and X-linked). Handles snv's and indels.

2) Options allow inclusion or exclusion of variants depending on quality score and membership of variant in dbSNP.

3) Identifies variants in genes already associated with a developmental brain phenotype. This saves you time. Why rediscover the wheel?

4) Provides direct links to additional brain-specific annotation you need the most. That means the Allen Brain Atlas, PubMed, Lynx, Mouse Genome Informatics, and the UCSC Genome Browser. If these sources don't know anything about your candidate gene, chances are no one does.

Features 1-3 are handled by SOLVE-Brain's command line interface.
Feature 4 is handled in the browser using HTML5 sessionStorage. You do not need to upload your data to someone else's server to use SOLVE-Brain.

Here's what you do:

1) Start with an annotated vcf of whole exome data. SOLVE-Brain runs at the command line to let you filter by pedigree, quality score, and dbSNP membership. It also generates a list of genes that are found in our Database of Developmental Brain Disorders (DBDB), and therefore known actors in disorders of brain development. This is ideal for quick analysis.

2) SOLVE-Brain's command line interface gives you variants in vcf format prioritized by your parameters. You also get an extracted list of genes of interest.

3) Then you use SOLVE-Brain's web interface on our website. Paste your genes of interest into the box and hit "Add".

4) SOLVE-Brain gives you direct links to sources of additional brain-specific annotations. No more going again and again to Allen Brain's search function...SOLVE-Brain does it for you.

Cite SOLVE-Brain

You are welcome to use SOLVE-Brain for your own research. We are preparing a manuscript describing the tool's features. In the meantime, please reference SOLVE-Brain at:

Get SOLVE-Brain

Simply clone SOLVE-Brain from GitHub like this:

$ git clone https://github.com/Paciorkowski-Lab/SOLVE-Brain.git