Codes for Intein-assisted Bisection Mapping (IBM)

Manuscript: "Intein-assisted bisection mapping systematically splits proteins for Boolean logic and inducibility engineering"

Repository for codes used in IBM experiments.

For analyzing Sanger sequencing results at the last stage of PCR products, please refer to the notebook:
identify_split_site.ipynb

For analyzing NGS data on final IBM libraries, please refer to the manual:
NGS_analysis manual.ipynb
which will provide an overview of steps

Note: For NGS analysis, check out dipseq for a better pipeline.

Dependencies

Licensed under the MIT License.

Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
IBM_seq_example		IBM_seq_example
filtered_fastq_files		filtered_fastq_files
images		images
raw_fastq_files		raw_fastq_files
results_per_fastq		results_per_fastq
results_per_target_protein		results_per_target_protein
.gitignore		.gitignore
LICENSE		LICENSE
NGS_alignment_time.txt		NGS_alignment_time.txt
NGS_analysis_manual.ipynb		NGS_analysis_manual.ipynb
NGS_step1_filter_fastq.ipynb		NGS_step1_filter_fastq.ipynb
NGS_step2_infer_spilt_site.ipynb		NGS_step2_infer_spilt_site.ipynb
NGS_step3_clean_up_data.ipynb		NGS_step3_clean_up_data.ipynb
README.md		README.md
example_bla_split_sites.csv		example_bla_split_sites.csv
identify_split_site.ipynb		identify_split_site.ipynb
target_protein_CDS_plus.fa		target_protein_CDS_plus.fa
target_protein_info.csv		target_protein_info.csv