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iGEM

Welcome to the iGEM repositories. In this you will find all of our bio-informatic and modeling scripts:

  • Run_BLAST.ipynb : a pipeline to run the BLAST algorithm from the NCBI server and read/filter the results. We used this pipaline to verify the guide RNA that we develop in order to avoid false positive in our detection

  • Target sequence extraction.ipynb : a pipeline to extract DNA sequence from protein name using different protein databases

  • Modeling.ipynb : kinetic modeling notebook of our LwCas13a SHERLOCK reaction

  • Paper_test_quantification.ipynb : semi-quantitative analysis of the results of our lateral flow assay

  • PyCCELL_PRFQT: the script to analyze plate reader data (and the .py version to import in other scripts)

  • SHERLOCK_modeling: Fitting of the experimental results gotten from SHERLOCK experiments using the kinetic model

  • SHERLOCK_probe_dilution: Plotting of the results gotten from the SHERLOCK experiments on probe concentration optimization