CRISPR detection

VC Victor Borin Centurion
AR Alessandro Rossi
EO Esteban Orellana
GG Gabriele Ghiotto
BK Balázs Kakuk
MM Maria Silvia Morlino
AB Arianna Basile
GZ Guido Zampieri
LT Laura Treu
SC Stefano Campanaro
ask Ask a question
Favorite

MinCED v0.4.2 [48] was used to identify clustered regularly interspaced short palindromic repeats (CRISPR) spacers in the dereplicated MAGs. A BLAST v2.6.0 [49] search for viral sequences recovered in this study against the spacers was performed using parameters including -task blastn-short, -gapopen 10, -gapextend 2, -penalty -1, -word_size 7, -perc_identity 100, as previously reported [50]. The results were filtered to include only those that matched the whole length of the spacer. To visualize interactions between Phages and Archaea, HoloViews v1.15.4 (https://github.com/holoviz/holoviews), along with Pandas (v2.3.1) and NumPy (v1.21) packages in python v3.6.13 were used. The phage coverage was estimated using CoverM v0.6.1 with the “contig” subcommand. To compare the presence of phages in different experiments for each virMAG, the abundance was divided by the total number of reads in each sample.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A