Bioinformatics Tools

  Sequence analysis tools
 
  * LOD Score Calculator for Sequence Modeling
    * Pairwise Protein Sequence Alignment (Using multiple substitution scoring matrixes)
    *
Simple Sequence Alignment(Using simple scoring scheme match/mismatch/gap)
    *
Sequence Fitting Alignment(To fit a shorter sequence into a longer one)
    *
Repeat Finder(To identify repeats in a string of DNA/protein sequence)     

  Cheminformatics tools
    * 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)