Giters

apcamargo / padloc

Locate antiviral defence systems in prokaryotic genomes

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

PADLOC: Prokaryotic Antiviral Defence LOCator

About

PADLOC is a software tool for identifying antiviral defence systems in prokaryotic genomes. PADLOC screens genomes against a database of HMMs and system classifications to find and annotate defence systems based on sequence homology and genetic architecture.

PADLOC can be installed and used via the command line or via our web server.

Citation

If you use PADLOC or PADLOC-DB please cite:

Payne, L. J., Todeschini, T. C., Wu, Y., Perry, B. J., Ronson, C. W., Fineran, P. C., Nobrega, F. L., Jackson, S. A. (2021) Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Research, 49, 10868-10878. doi: https://doi.org/10/gzgh

The HMMs in PADLOC-DB were built/curated using data from various sources, we encourage you to also give credit to these groups by citing them too.

Installation

Conda (recommended)

It is recommended that PADLOC be installed via conda.

# Install PADLOC into a new conda environment
conda create -n padloc -c conda-forge -c bioconda -c padlocbio padloc
# Activate the environment
conda activate padloc
# Download the latest database
padloc --db-update

GitHub

The latest development version of PADLOC can be installed by cloning this GitHub repository and installing the dependencies manually.

# Clone repo to $HOME
git clone https://github.com/padlocbio/padloc $HOME/padloc
# Add to $PATH
export PATH="$HOME/padloc/bin:$PATH"
# Download the latest database
padloc --db-update

Examples

# BASIC: Search an amino acid fasta file with accompanying GFF annotations
padloc --faa genome.faa --gff features.gff
# BASIC: Search a nucleic acid fasta file, identifying CDS with prodigal
padloc --fna genome.fna
# BASIC: Include CRISPR array information from CRISPRDetect output
padloc --faa genome.faa --gff features.gff --crispr arrays.gff
# INTERMEDIATE: Use multiple cpus and save output to a different directory
padloc --faa genome.faa --gff features.gff --outdir path_to_output --cpu 4
# ADVANCED: Use your own HMMs and system models
padloc --faa genome.faa --gff features.gff --data path_to_database

Test

# Try running PADLOC on the test data provided
padloc --faa padloc/test/GCF_001688665.2.faa --gff padloc/test/GCF_001688665.2.gff
padloc --fna padloc/test/GCF_004358345.1.fna

Options

General:
    --help            Print this help message
    --version         Print version information
    --citation        Print citation information
    --check-deps      Check that dependencies are installed
    --debug           Run with debug messages
Database:
    --db-list         List all PADLOC-DB releases
    --db-install [n]  Install specific PADLOC-DB release [n]
    --db-update       Install latest PADLOC-DB release
    --db-version      Print database version information
Input:
    --faa [f]         Amino acid FASTA file (only valid with [--gff])
    --gff [f]         GFF file (only valid with [--faa])
    --fna [f]         Nucleic acid FASTA file
    --crispr [f]      CRISPR array input file (.gff from CRISPRDetect)
Output:
    --outdir [d]      Output directory
Optional:
    --data [d]        Data directory
    --cpu [n]         Use [n] CPUs (default '1')
    --raw-out         Include a summarised raw output file
    --fix-prodigal    Set this flag when providing an FAA and GFF file 
                      generated with prodigal to force fixing of sequence IDs

Output

File Description
*.domtblout Domain table file generated by HMMER.
*_prodigal.faa Amino acid FASTA file generated by prodigal.
*_prodigal.gff GFF annotation file generated by prodigal.
*_padloc.csv PADLOC output file for identified defence systems.
*_padloc.gff GFF annotation file for identified defence systems.

Interpreting Output

Column Description
system.number Distinct system number.
seqid Sequence ID of the contig.
system Name of the system identified.
target.name Protein ID.
hmm.accession PADLOC HMM accession number.
hmm.name PADLOC HMM name.
protein.name Defence system protein name.
full.seq.E.value Full sequence E-value. From the HMMER Documentation: "The E-value is a measure of statistical significance. The lower the E-value, the more significant the hit."
domain.iE.value Domain E-value. From the HMMER Documentation: "If the full sequence E-value is significant but the single best domain E-value is not, the target sequence is probably a multidomain remote homolog".
target.coverage Fraction of the target sequence aligning to the HMM.
hmm.coverage Fraction of the HMM aligning to the target sequence.
start Start position of the target sequence in the contig.
end End position of the target sequence in the contig.
strand Strand; forward (+) or reverse (-)
target.description Target sequence descrition taken from the input file.
relative.position Relative position of the target sequence in the contig.
contig.end Relative position of the last sequence in the contig.
all.domains Concatenated list of all domains identified with HMMER.
best.hits Top 5 hits identified with HMMER.

PADLOC-DB

The HMMs and defence system models used by PADLOC are available from the repository PADLOC-DB. The latest version of the database can be downloaded by running padloc --db-update. Alternatively, a custom database can be specified with --data [d], refer to PADLOC-DB for more information about configuring a custom database.

FAQ

  • What are the requirements for an FAA/GFF file pair as input?

    The GFF file should conform to the GFF3 specification. Each sequence in the FAA file is matched to an entry in the GFF file based on its ID attribute e.g. for the following sequence:

    >WP_000000001.1 molybdopterin-dependent oxidoreductase, partial [Escherichia coli]
AAAAAAAGLSVPGVARAVLVSRKPSNGIKAPCRFCGTGCGVLVGTQQGRVVACQGDPDAPVNRGLNCIKG
YFLPKIMYGKDRLTQPLLRMKNGKYDKEGEFTPITWDQAFDVMEEKFKTALKEKGPESIGMFGSGQWTIW
EGYAASKLFKAGFRSNNIDPNARHCMASAVVGFMRTFGMDEPMGCYDDIEQADAFVLWGANMAEMHPILW
SRITNRRLSN

    The corresponding entry in the GFF file should contain an ID attribute of the form:

    ID=WP_000000001.1 or ID=cds-WP_000000001.1

    FAA/GFF combinations that are known to work 'out-of-the-box' are from genomes annotated with:

  • Why are there parsing failures when using a GFF file from prokka?

    The following warning may be thrown when using a GFF file generated by prokka:

    Warning: 46324 parsing failures.
 row col  expected    actual         file
2612  -- 9 columns 1 columns 'prokka.gff'
2613  -- 9 columns 1 columns 'prokka.gff'
2614  -- 9 columns 1 columns 'prokka.gff'
2615  -- 9 columns 1 columns 'prokka.gff'
2616  -- 9 columns 1 columns 'prokka.gff'
.... ... ......... ......... ............
See problems(...) for more details.

    This is because these GFF files are appended with the contig sequences of the annotated genome. This warning can be avoided by removing the contig sequences from the GFF file with:

    sed '/^##FASTA/Q' prokka.gff > nosequence.gff

  • Why can't I use a nucleotide FASTA file with < 100 kbp?

    According to Prodigal's own documentation, sequences < 100 kbp are "too short to gather enough statistics to predict genes well". To avoid issues arising from this, PADLOC won't try to run prodigal over anything < 100 kbp.

    If you know what you're doing then you can use Prodigal or another gene prediction program to generate your own FAA and GFF files to then use with PADLOC.

Issues

Bugs and feature requests can be submitted to the Issues tab (see Sample bug report).

Dependencies

These dependencies are installed automatically when using conda.

Mandatory

  • R >= 4.1.0
    R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
  • HMMER >= 3.3.2
    Finn, R.D., Clements, J., and Eddy, S.R. (2011). HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39, W29–W37.

Optional

  • Prodigal >= 2.6.3
    Hyatt, D., Chen, GL., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119.

References

The HMMs in PADLOC-DB were built/curated using data from various sources, we encourage you to also give credit to these groups by citing them too:

Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G. and Sorek, R. (2018) Systematic discovery of antiphage defense systems in the microbial pangenome. Science, 359, eaar4120. doi: 10/ggqhzm

Millman, A., Melamed, S., Amitai, G. and Sorek, R. (2020) Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems. Nature Microbiology, 5, 1608–1615. doi: 10/gg84nk

Couvin, D., Bernheim, A., Toffano-Nioche, C., Touchon, M., Michalik, J., Néron, B., Rocha, E. P. C., Vergnaud, G., Gautheret, D. and Pourcel, C. (2018) CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res, 46, W246–W251. doi: 10/ggdjdf

Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J. J., Charpentier, E., Cheng, D., Haft, D. H., Horvath, P., et al. (2020) Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol, 18, 67–83. doi: 10/ggkfgj

Shah, S. A., Alkhnbashi, O. S., Behler, J., Han, W., She, Q., Hess, W. R., Garrett, R. A. and Backofen, R. (2019) Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families. RNA Biology, 16, 530–542. doi: 10/ggqv9p

Shmakov, S. A., Makarova, K. S., Wolf, Y. I., Severinov, K. V. and Koonin, E. V. (2018) Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. PNAS, 115, E5307–E5316. doi: 10/gdpqwq

Russel, J., Pinilla-Redondo, R., Mayo-Muñoz, D., Shah, S. A. and Sørensen, S. J. (2020) CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci. The CRISPR Journal, 3, 462–469. doi: 10/gshm

Gao, L., Altae-Tran, H., Böhning, F., Makarova, K. S., Segel, M., Schmid-Burgk, J. L., Koob, J., Wolf, Y. I., Koonin, E. V. and Zhang, F. (2020) Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science, 369, 1077–1084. doi: 10/gpsx

Makarova, K. S., Timinskas, A., Wolf, Y. I., Gussow, A. B., Siksnys, V., Venclovas, Č. and Koonin, E. V. (2020) Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense. Nucleic Acids Res, 48, 8828–8847. doi: 10/gg7qx6

Bouchard, J. D., Dion, E., Bissonnette, F. and Moineau, S. (2002) Characterization of the Two-Component Abortive Phage Infection Mechanism AbiT from Lactococcus lactis. Journal of Bacteriology, 184, 6325–6332. doi: 10/btq97w

Parma, D. H., Snyder, M., Sobolevski, S., Nawroz, M., Brody, E. and Gold, L. (1992) The Rex system of bacteriophage lambda: tolerance and altruistic cell death. Genes Dev., 6, 497–510. doi: 10/b9xpsb

Jabbar, M. A. and Snyder, L. (1984) Genetic and physiological studies of an Escherichia coli locus that restricts polynucleotide kinase- and RNA ligase-deficient mutants of bacteriophage T4. Journal of Virology, 51, 522–529. doi: 10/gndc4t

Cram, D., Ray, A. and Skurray, R. (1984) Molecular analysis of F plasmid pif region specifying abortive infection of T7 phage. Mol Gen Genet, 197, 137–142. doi: 10/fg7s8g

Smith, H. S., Pizer, L. I., Pylkas, L. and Lederberg, S. (1969) Abortive Infection of Shigella dysenteriae P2 by T2 Bacteriophage. Journal of Virology, 4, 162–168. doi: 10/gndc4r

Dai, G., Su, P., Allison, G. E., Geller, B. L., Zhu, P., Kim, W. S. and Dunn, N. W. (2001) Molecular Characterization of a New Abortive Infection System (AbiU) from Lactococcus lactisLL51-1. Applied and Environmental Microbiology, 67, 5225–5232. doi: 10/cwbxdg

Lindahl, G., Sironi, G., Bialy, H. and Calendar, R. (1970) Bacteriophage Lambda; Abortive Infection of Bacteria Lysogenic for Phage P2. PNAS, 66, 587–594. doi: 10/fkgq7x

Bergsland, K. J., Kao, C., Yu, Y. T. N., Gulati, R. and Snyder, L. (1990) A site in the T4 bacteriophage major head protein gene that can promote the inhibition of all translation in Escherichia coli. Journal of Molecular Biology, 213, 477–494. doi: 10/fv36tb

Durmaz, E. and Klaenhammer, T. R. (2007) Abortive Phage Resistance Mechanism AbiZ Speeds the Lysis Clock To Cause Premature Lysis of Phage-Infected Lactococcus lactis. Journal of Bacteriology, 189, 1417–1425. doi: 10/dnndhw

Haaber, J., Moineau, S., Fortier, L. C. and Hammer, K. (2008) AbiV, a Novel Antiphage Abortive Infection Mechanism on the Chromosome of Lactococcus lactis subsp. cremoris MG1363. Applied and Environmental Microbiology, 74, 6528–6537. doi: 10/cnwcq7

Emond, E., Dion, E., Walker, S. A., Vedamuthu, E.R., Kondo, J.K. and Moineau, S. (1998) AbiQ, an Abortive Infection Mechanism fromLactococcus lactis. Applied and Environmental Microbiology, 64, 4748–4756. doi: 10/gndc4p

Domingues, S., Chopin, A., Ehrlich, S. D. and Chopin, M. C. (2004) The Lactococcal Abortive Phage Infection System AbiP Prevents both Phage DNA Replication and Temporal Transcription Switch. Journal of Bacteriology, 186, 713–721. doi: 10/bjjwc6

Prevots, F. and Ritzenthaler, P. (1998) Complete Sequence of the New Lactococcal Abortive Phage Resistance Gene abiO. Journal of Dairy Science, 81, 1483–1485. doi: 10/cg69rg

Prévots, F., Tolou, S., Delpech, B., Kaghad, M. and Daloyau, M. (1998) Nucleotide sequence and analysis of the new chromosomal abortive infection gene abiN of Lactococcus lactis subsp. cremoris S114. FEMS Microbiology Letters, 159, 331–336. doi: 10/c94sd6

Deng, Y. M., Liu, C. Q. and W. Dunn, N. (1999) Genetic organization and functional analysis of a novel phage abortive infection system, AbiL, from Lactococcus lactis. Journal of Biotechnology, 67, 135–149. doi: 10/bwc9k8

Emond, E., Holler, B. J., Boucher, I., Vandenbergh, P. A., Vedamuthu, E. R., Kondo, J. K. and Moineau, S. (1997) Phenotypic and genetic characterization of the bacteriophage abortive infection mechanism AbiK from Lactococcus lactis. Applied and Environmental Microbiology, 63, 1274–1283. doi: 10/gndc4n

Deng, Y. M., Harvey, M. L., Liu, C. Q. and Dunn, N. W. (1997) A novel plasmid-encoded phage abortive infection system from Lactococcus lactis biovar. diacetylactis. FEMS Microbiology Letters, 146, 149–154. doi: 10/d24tcq

Su, P., Harvey, M., Im, H. J. and Dunn, N. W. (1997) Isolation, cloning and characterisation of the abiI gene from Lactococcus lactis subsp. lactis M138 encoding abortive phage infection. Journal of Biotechnology, 54, 95–104. doi: 10/ckwmpp

Prévots, F., Daloyau, M., Bonin, O., Dumont, X. and Tolou, S. (1996) Cloning and sequencing of the novel abortive infection gene abiH of Lactococcus lactis ssp. lactis biovar. diacetylactis S94. FEMS Microbiology Letters, 142, 295–299. doi: 10/dvjcb5

O’Connor, L., Coffey, A., Daly, C. and Fitzgerald, G. F. (1996) AbiG, a genotypically novel abortive infection mechanism encoded by plasmid pCI750 of Lactococcus lactis subsp. cremoris UC653. Applied and Environmental Microbiology, 62, 3075–3082. doi: 10/gndc4m

Garvey, P., Fitzgerald, G. F. and Hill, C. (1995) Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Applied and Environmental Microbiology, 61, 4321–4328. doi: 10/gndc3x

Dy, R. L., Przybilski, R., Semeijn, K., Salmond, G. P. C. and Fineran, P. C. (2014) A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism. Nucleic Acids Research, 42, 4590–4605. doi: 10/f5zkmw

McLandsborough, L.A., Kolaetis, K. M., Requena, T. and McKay, L. L. (1995) Cloning and characterization of the abortive infection genetic determinant abiD isolated from pBF61 of Lactococcus lactis subsp. lactis KR5. Applied and Environmental Microbiology, 61, 2023–2026. doi: 10/gndc4j

Garvey, P., Fitzgerald, G. F. and Hill, C. (1995) Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Applied and Environmental Microbiology, 61, 4321–4328. doi: 10/gndc3x

Anba, J., Bidnenko, E., Hillier, A., Ehrlich, D. and Chopin, M. C. (1995) Characterization of the lactococcal abiD1 gene coding for phage abortive infection. Journal of Bacteriology, 177, 3818–3823. doi: 10/gndc3w

Durmaz, E., Higgins, D. L. and Klaenhammer, T. R. (1992) Molecular characterization of a second abortive phage resistance gene present in Lactococcus lactis subsp. lactis ME2. Journal of Bacteriology, 174, 7463–7469. doi: 10/gndc3v

Parreira, R., Ehrlich, S. D. and Chopin, M. C. (1996) Dramatic decay of phage transcripts in lactococcal cells carrying the abortive infection determinant AbiB. Molecular Microbiology, 19, 221–230. doi: 10/b835bf

Cluzel, P. J., Chopin, A., Ehrlich, S. D. and Chopin, M. C. (1991) Phage abortive infection mechanism from Lactococcus lactis subsp. lactis, expression of which is mediated by an Iso-ISS1 element. Applied and Environmental Microbiology, 57, 3547–3551. doi: 10/gndc3t

Dinsmore, P. K. and Klaenhammer, T. R. (1994) Phenotypic Consequences of Altering the Copy Number of abiA, a Gene Responsible for Aborting Bacteriophage Infections in Lactococcus lactis. Applied and Environmental Microbiology, 60, 1129–1136. doi: 10/gndc3s

Owen, S. V., Wenner, N., Dulberger, C. L., Rodwell, E. V., Bowers-Barnard, A., Quinones-Olvera, N., Rigden, D. J., Rubin, E. J., Garner, E. C., Baym, M., et al. (2021) Prophages encode phage-defense systems with cognate self-immunity. Cell Host & Microbe, 29, 1620-1633. doi: 10/g29b

Bari, S. M. N., Chou-Zheng, L., Howell, O., Cater, K., Dandu, V. S., Thomas, A., Aslan, B., and Hatoum-Aslan, A. (2021). A unique mode of nucleic acid immunity performed by a single multifunctional enzyme. bioRxiv. doi: 10/gkw6wr

Burroughs A. M., Ando Y., Aravind L. (2014) New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. WIREs RNA. 5, 141–181. doi: 10/gfkh7c

Makarova, K. S., Wolf, Y. I., van der Oost, J., and Koonin, E. V. (2009). Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct, 4, 29. doi: 10/cvfhm6

Burroughs, A. M., Iyer, L. M., and Aravind, L. (2013). Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes. Biology Direct 8, 13. doi: 10/f46qcd

Zeng, Z., Chen, Y., Pinilla-Redondo, R., Shah, S. A., Zhao, F., Wang, C., Hu, Z., Zhang, C., Whitaker, R. J., She, Q., et al. (2021). A short prokaryotic argonaute cooperates with membrane effector to confer antiviral defense. bioRxiv. doi: 10//hgr9

Mestre, M. R., González-Delgado, A., Gutiérrez-Rus, L. I., Martínez-Abarca, F., and Toro, N. (2020). Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems. Nucleic Acids Research, 48, 12632–12647. doi: 10/fzk3

Millman, A., Bernheim, A., Stokar-Avihail, A., Fedorenko, T., Voichek, M., Leavitt, A., Oppenheimer-Shaanan, Y., and Sorek, R. (2020). Bacterial Retrons Function In Anti-Phage Defense. Cell, 183, 1551-1561.e12. doi: 10/ghjct3

Bernheim, A., Millman, A., Ofir, G., Meitav, G., Avraham, C., Shomar, H., Rosenberg, M. M., Tal, N., Melamed, S., Amitai, G., et al. (2021). Prokaryotic viperins produce diverse antiviral molecules. Nature, 589, 120–124. doi: 10/d9ss

Goldfarb, T., Sberro, H., Weinstock, E., Cohen, O., Doron, S., Charpak‐Amikam, Y., Afik, S., Ofir, G., and Sorek, R. (2015). BREX is a novel phage resistance system widespread in microbial genomes. EMBO J, 34, 169–183. doi: 10/f2wkj3

Ofir, G., Melamed, S., Sberro, H., Mukamel, Z., Silverman, S., Yaakov, G., Doron, S., and Sorek, R. (2018). DISARM is a widespread bacterial defence system with broad anti-phage activities. Nat Microbiol, 3, 90–98. doi: 10/ggnszb

Yuan, Y., Hutinet, G., Valera, J. G., Hu, J., Hillebrand, R., Gustafson, A., Iwata-Reuyl, D., Dedon, P. C., and de Crécy-Lagard, V. (2018). Identification of the minimal bacterial 2′-deoxy-7-amido-7-deazaguanine synthesis machinery. Molecular Microbiology, 110, 469–483. doi: 10/gfft6b

Thiaville, J. J., Kellner, S. M., Yuan, Y., Hutinet, G., Thiaville, P. C., Jumpathong, W., Mohapatra, S., Brochier-Armanet, C., Letarov, A. V., Hillebrand, R., et al. (2016). Novel genomic island modifies DNA with 7-deazaguanine derivatives. Proc Natl Acad Sci USA, 113, E1452–E1459. doi: 10/ggr4f7

Tong, T., Chen, S., Wang, L., Tang, Y., Ryu, J. Y., Jiang, S., Wu, X., Chen, C., Luo, J., Deng, Z., et al. (2018). Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria. Proc Natl Acad Sci USA, 115, E2988–E2996. doi: 10/gdbj2n

Xu, T., Yao, F., Zhou, X., Deng, Z., and You, D. (2010). A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella. Nucleic Acids Research, 38, 7133–7141. doi: 10/d5zqcp

Xiong, L., Liu, S., Chen, S., Xiao, Y., Zhu, B., Gao, Y., Zhang, Y., Chen, B., Luo, J., Deng, Z., et al. (2019). A new type of DNA phosphorothioation-based antiviral system in archaea. Nat Commun, 10, 1688. 10/ggctjz

Xiong, X., Wu, G., Wei, Y., Liu, L., Zhang, Y., Su, R., Jiang, X., Li, M., Gao, H., Tian, X., et al. (2020). SspABCD–SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities. Nat Microbiol, 5, 917–928. 10/ggq8nb

Wang, S., Wan, M., Huang, R., Zhang, Y., Xie, Y., Wei, Y., Ahmad, M., Wu, D., Hong, Y., Deng, Z., et al. (2021). SspABCD-SspFGH Constitutes a New Type of DNA Phosphorothioate-Based Bacterial Defense System. MBio, 12, e00613-21. 10/gbsw

The relevant refences for individual HMMs can be found by inspecting the hmm_meta.txt file provided with PADLOC-DB.

License

This software and data is available as open source under the terms of the MIT License.

About

Locate antiviral defence systems in prokaryotic genomes

License:MIT License

Languages

Language:R 65.9%Language:Shell 34.1%