Bioinformatics Tools & Data

Ontology

GO slim creation pipeline – The files and documents collected here are described in the manuscript “Automatic, context-specific generation of Gene Ontology slims” (MJ Davis, MS Sehgal and MA Ragan, BMC Bioinformatics 11:498, 2010)
Small Molecule Ontology – The files and documents collected here are described in the manuscript “A Semantic Web for small molecules and their biological targets” (JY Choi, MJ Davis, AF Newman and MA Ragan, Journal of Chemical Information and Modeling 50:732-741, 2010)

 

Other

Reordering genes: reorders a list of gene names according to their UniGene names
Cane EcoGenomics

GEC robustness in LGT graphs by TF-IDF (Cong et al.): High resolution network diagrams for BA and BAC datasets

Networks_new_144.zip
Description: All LGT networks for the BAC dataset are included. k=20, 30, 40; G=2k. The sequences are grouped by order, each order contains 6 sequences (bacterial genomes).

network_143L2.zip
Description: All LGT networks for the BA dataset are inculded. k=20, 25, 30, 35, 40; G=2k. The sequences are grouped by phylum.

Networks_143L3.zip
Description: All LGT networks for the BA dataset are included. k=20, 25, 30, 35, 40; G=2k. The sequences are grouped by class.

 

To add to this list, please email m.ragan@imb.uq.edu.au.

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