Our open-source bioinformatics tools that have been published

  1. CRISPR-DT (A web application for designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity) (Bioinformatics, in press)
  2. CRISPR-RT (A web application for designing CRISPR-C2c2 crRNA with improved target specificity) (Bioinformatics, 34:117-119)
  3. JNSViewer (JavaScript-based Sequence Viewer for DNA/RNA Secondary Structures) (PLoS ONE, 12: e0179040)
  4. CRF (CRISPR Finder by Random Forest) (PeerJ, 5:e3219)
  5. CT-Finder (Optimal Target Prediction and Visualization for Genome Editing with CRISPR/Cas Systems) (Scientific Reports, 6:25516)
  6. detectMITE (Scientific Reports, 6:19688)
  7. mirPRo (Scientific Reports, 5:14617)
  8. CADBURE (Scientific Reports, 5:13443)
  9. Poly(A) Toolkit (Methods Mol Biol, 1255:25-37)
  10. detectIR (PLOS One, 9(11):e0113349)
  11. Random Forest and SVM Classifier (PLOS One, 9(8):e104049)
  12. SCOPE++ (Sequence Classification Of homoPolymer Emissions) (Genomics, 104:157-162)
  13. Palindrome (also known as findIR) (Bioinformatics, 30:887-888)
  14. AFST (Abnormality Filtering and Sequence Trimming for ESTs) (BMC Biotechnology, 12:6)
  15. CBrowse (Bioinformatics, 28:2382-2384)

Our bioinformatics tools under development that can be used or tested

  1. SeqViewer
  2. SCRAP++: Sequence Cleaning and Removal of Adapter Sequences using Profile HMMs
  3. RNA Dynamic Miner
  4. RNA Structure Miner