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modify blastn parameters to match those in Shmakov et al NAR 2023 #1

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pentamorfico wants to merge 3 commits into Russel88:master from pentamorfico:master

pentamorfico commented Feb 20, 2024

Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems

Repeat-like sequences were detected using BLASTN with the following parameters: reward 3, penalty -2, gapextend 5, gapopen 5, word_size 6, dust set to ‘no’, and e-value 10.

pentamorfico added 3 commits

February 20, 2024 13:48


          modify blastn parameters

485ae19


          modify adj cluster to only retain repeats from the same type

68f9206


          keep repeats >40%seq id, similar type

a4fcef0

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