Team III Functional Annotation Group: Difference between revisions
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=='''References'''== | =='''References'''== | ||
Barrangou R. The roles of CRISPR-Cas systems in adaptive immunity and beyond. Curr Opin Immunol. 2015;32:36–41. doi:10.1016/j.coi.2014.12.008 | |||
Edgar, Robert C. "PILER-CR: fast and accurate identification of CRISPR repeats." BMC bioinformatics 8.1 (2007): 18. | |||
Alcock, Brian P., et al. "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database." Nucleic acids research 48.D1 (2020): D517-D525. | |||
Liu, Bo, et al. "VFDB 2019: a comparative pathogenomic platform with an interactive web interface." Nucleic acids research 47.D1 (2019): D687-D692. | |||
Revision as of 19:28, 9 April 2020
Group Members - Allison, Bengu, Cheng, Pallavi Misra
Introduction
Initial Pipeline
Homology Tools
CARD-RGI
VFDB
Ab-initio - Tools
PILERCR
Final Pipeline
Results
CARD-RGI
$ rgi -i <input_file> -o <output_file>
VFDB
$ makeblastdb -in <input_db> -parse_seqids -blastdb_version 5 -dbtype nucl -out <name_db> $ blastn -db <name_db> -query <input_file> -out <output_file> -max_hsps 1 -max_target_seqs 1 -num_threads 4 -evalue 1e-5
PILERCR
$ ./pilercr -in <input_file> -out <output_file>
References
Barrangou R. The roles of CRISPR-Cas systems in adaptive immunity and beyond. Curr Opin Immunol. 2015;32:36–41. doi:10.1016/j.coi.2014.12.008 Edgar, Robert C. "PILER-CR: fast and accurate identification of CRISPR repeats." BMC bioinformatics 8.1 (2007): 18. Alcock, Brian P., et al. "CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database." Nucleic acids research 48.D1 (2020): D517-D525. Liu, Bo, et al. "VFDB 2019: a comparative pathogenomic platform with an interactive web interface." Nucleic acids research 47.D1 (2019): D687-D692.