Package: sgrna-designer
sgrna_designerPython library to design sgRNAs for CRISPR tiling screensThe primary function of this package isdesign_sgrna_tiling_library, in which you can input a list of
ensembl transcript IDs, specify a region of interest (e.g. three_prime_UTR) and get all sgRNAs
tiling those transcript regions.Installpip install git+https://github.com/gpp-rnd/sgrna_designer.git#egg=sgrna_designerAn exampleIn this example we'll design sgRNAs tiling the 3' UTR of PDL1 (CD274) and BRAFNote: You must also havepandas installedto run this tutorialfrom sgrna_designer.design import design_sgrna_tiling_library

target_transcripts = ['ENST00000381577', 'ENST00000644969'] # [PDL1, BRAF]Note the design function is agnostic to CRISPR enzyme and pam preferences, so you must specifiy the
following parameters in a design run:region: broad region you are trying to target (e.g. UTR)region: more specific region you are trying to target (e.g. three_prime_UTR)expand_3prime: amount to expand region in 3' directionexpand_5prime: amount to expand region in 5' directioncontext_len: length of context sequencepam_start: position of PAM start relative to the context sequencepam_len: length of PAMsgrna_start: position of sgRNA relative to context sequencesgrna_len: length of sgRNA sequencepams: PAMs to targetsg_positions: positions within the sgRNA to annotate and target
(e.g. [4,8] for nucleotides 4 and 8 of the sgRNA for a base editing window)sgrna_designs = design_sgrna_tiling_library(target_transcripts, region_parent='UTR',
                                            region='three_prime_UTR', expand_3prime=30,
                                            expand_5prime=30, context_len=30, pam_start=-6,
                                            pam_len=3, sgrna_start=4, sgrna_len=20,
                                            pams=['AGG', 'CGG', 'TGG', 'GGG'],
                                            sg_positions=[4, 8], flag_seqs=['TTTT', 'CGTCTC', 'GAGACG'],
                                            flag_seqs_start=['TCTC', 'AGACG'], flag_seqs_end=['GAGAC'])
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}</style>context_sequencepam_sequencesgrna_sequencesgrna_global_startsgrna_global_4sgrna_global_8sgrna_strandobject_typetranscript_strandtranscript_idchromosomeregion_idregion_startregion_end0CATTGGAACTTCTGATCTTCAAGCAGGGATAGGGGAACTTCTGATCTTCAAGC5467872546787554678791three_prime_UTR1ENST000003815779ENST00000381577546786354705541ATTGGAACTTCTGATCTTCAAGCAGGGATTGGGGAACTTCTGATCTTCAAGCA5467873546787654678801three_prime_UTR1ENST000003815779ENST00000381577546786354705542CTTCAAGCAGGGATTCTCAACCTGTGGTTTTGGAAGCAGGGATTCTCAACCTG5467888546789154678951three_prime_UTR1ENST000003815779ENST00000381577546786354705543GCAGGGATTCTCAACCTGTGGTTTAGGGGTAGGGGATTCTCAACCTGTGGTTT5467894546789754679011three_prime_UTR1ENST000003815779ENST00000381577546786354705544CAGGGATTCTCAACCTGTGGTTTAGGGGTTGGGGATTCTCAACCTGTGGTTTA5467895546789854679021three_prime_UTR1ENST000003815779ENST0000038157754678635470554.............................................845GCTCAGGTCCCTTCATTTGTACTTTGGAGTTGGAGGTCCCTTCATTTGTACTT140719570140719567140719563-1three_prime_UTR-1ENST000006449697ENST00000644969140719337140726493846TATAACAGAAAATATTGTTCAGTTTGGATATGGACAGAAAATATTGTTCAGTT140719522140719519140719515-1three_prime_UTR-1ENST000006449697ENST00000644969140719337140726493847ATTGTTCAGTTTGGATAGAAAGCATGGAGATGGTTCAGTTTGGATAGAAAGCA140719509140719506140719502-1three_prime_UTR-1ENST000006449697ENST00000644969140719337140726493848TATTTAAAAACTGTATTATATAAAAGGCAAAGGTAAAAACTGTATTATATAAA140719426140719423140719419-1three_prime_UTR-1ENST000006449697ENST00000644969140719337140726493849CTGCTATAATAAAGATTGACTGCATGGAGATGGTATAATAAAGATTGACTGCA140719360140719357140719353-1three_prime_UTR-1ENST000006449697ENST00000644969140719337140726493850 rows × 14 columns