Sequence analysis tools
* LOD Score Calculator for Sequence Modeling
* Pairwise Protein Sequence Alignment (Using multiple substitution scoring matrixes)
Sequence Alignment(Using simple scoring scheme match/mismatch/gap)
* Sequence Fitting Alignment(To fit a shorter sequence into a longer one)
Finder(To identify repeats in a string of DNA/protein sequence)
* PubChemSR v3.6.0 (http://sourceforge.net/projects/pubchemsr) (Released on 3/31/2016)
(Windows-based application for searching & downloading data from NCBI's PubChem Chemical databases)
Demonstration Video (More on the PubChemSR homepage)
* Tox21 Chem Enrichment
(Web-based chemical annotation enrichment tool; collaboration with Dr. Scott Auerbach at NIH/NIEHS)
Literature mining tools
* SciMiner - Bio-NLP (Natural Language Processing) web-application for finding molecular target (gene/protein) in biomedical literatures and functional enrichment analyses (Gene,
GO, MeSH, Pathway, and PPI).
* VO-SciMiner (Brucella vaccine literature indexed with an extended version of SciMiner using Vaccine Ontology; collaboration with Dr. Yongqun Oliver He at University of Michigan).
Other web tools and resources
* Diabetic Neuropathy Microarray Knowledge-Base (DNMKB)
* microRNA world for diabetes (Go to Tools menu to analyze predicted structures of miRNA)
* ID conversion (to interconvert NCBI Entrez Gene IDs and Symbols and to extract their annotated Gene Ontology terms and KEGG pathways)
* ROS-Diabetes (Provides a comprehensive list of ROS-Diabetes related targets (genes/proteins) mined from the biomedical literature by SciMiner).
* GOODIES (Biological interpretation program for Microarray clustering results based on Gene-Ontology)