PYGR: Python Graph Database for Bioinformatics
From the website:
Pygr is open source software designed to make it easy to do powerful sequence and comparative genomics analyses, even with extremely large multi-genome alignments.
- Bioinformatics tools for sequence analysis and comparative genomics such as sequence databases, search methods such as BLAST, repeat-masking, megablast, etc., sequence annotation databases and annotation query, and sequence alignment datasets.
- Data namespace for accessing a given resource with seamless data relationship management. Easy data sharing that includes transparent access over network protocols.
- High performance graph representation of interval data
If anyone has any spare grant money must lying around for graduate student work, it would be real interesting to see an inter-disciplinary history on graph databases.
We may not be able to avoid re-inventing the wheel but perhaps we could re-invent stronger wheels more quickly.