Package: conodictor
ConoDictor: A fast and accurate prediction and classification tool for conopeptidesImportantIf using conodictor and have issue likeCONODB issue, please update to v2.3.6 that provide a fix.conodictor v2.3.6 introduce the -d option to specify the path to the db folder containing HMM and PSSM files for classification.This is a temporary solution while I am working on the next big release. Thanks.IntroductionCone snails are among the richest sources of natural peptides with promising pharmacological and therapeutic applications. With the reduced costs of RNAseq, scientists now heavily rely on venom gland transcriptomes for the mining of novel bioactive conopeptides, but the bioinformatic analyses often hamper the discovery process.ConoDictor 2 is a standalone and user-friendly command-line program. We have updated the program originally published as a web server 10 years ago using novel and updated tools and algorithms and improved our classification models with new and higher quality sequences. ConoDictor 2 is now more accurate, faster, multiplatform, and able to deal with a whole cone snail venom gland transcriptome (raw reads or contigs) in a very short time.The only input ConoDictor 2 requires is the assembled transcriptome or the raw reads file either in DNA or amino acid: the used alphabet is automatically recognized. ConoDictor 2 runs predictions directly on the proteins file (submitted or dynamically generated) and tries to report the longest conopeptide precursor-like sequence.InstallationInstall from PipYou will have first to installHMMER 3andPftoolsto be able to run conodictor.pipinstallconodictorUsing containersDockerAccessible athttps://hub.docker.com/u/ebedthanor onBioContainers.dockerpullebedthan/conodictor:latest
dockerrunebedthan/conodictor:latestconodictor-hExample of a rundockerrun--rm=True-v$PWD:/data-u$(id-u):$(id-g)ebedthan/conodictor:latestconodictor--out/data/outdir/data/input.fa.gzSeehttps://staph-b.github.io/docker-builds/run_containers/for more informations on how to properly run a docker container.SingularityThe singularity container does not need admin privileges making it
suitable for university clusters and HPC.singularitybuildconodictor.sifdocker://ebedthan/conodictor:latest
singularityexecconodictor.sifconodictor-hInstall from source# Download ConoDictor development versiongitclonehttps://github.com/koualab/conodictor.gitconodictor# Navigate to directorycdconodictor# Install with poetry: see https://python-poetry.orgpoetryinstall--no-dev# Enter the Python virtual environment withpoetryshell# Test conodictor is correctly installedconodictor-hIf you do not want to go into the virtual environment just do:poetryrunconodictor-hTestTypeconodictor -hand it should output something like:usage: conodictor [options] <FILE>

optional arguments:
  -o DIR, --out DIR   output result to DIR [ConoDictor]
  --mlen INT          minimum length of sequences to be considered [off]
  --ndup INT          minimum occurence sequences to be considered [off]
  --faa               dump a fasta file of matched sequences [false]
  --filter            only keep sequences matching sig, pro and mat regions [false]
  -a, --all           add unclassified sequences in result [false]
  -j INT, --cpus INT  number of threads [1]
  --force             re-use output directory [false]
  -q, --quiet         decrease program verbosity
  -v, --version       show program's version number and exit
  -h, --help          show this help message and exit

Citation: Koua et al., 2021, Bioinformatics AdvancesInvoking conodictorconodictorfile.fa.gz
conodictor--outoutfolder--cpus4--mlen51file.faOutput filesThe comma separeted-values file summary.csv can be easily viewed with any office suite,
or text editor.sequence,hmm_pred,pssm_pred definitive_pred
SEQ_ID_1,A,A,A
SEQ_ID_2,B,D,CONFLICT B and D
SEQ_ID_3,O1,O1,O1
...CitationWhen using ConoDictor2 in your work, you should cite:Dominique Koua, Anicet Ebou, Sébastien Dutertre, Improved prediction of conopeptide superfamilies with ConoDictor 2.0, Bioinformatics Advances, Volume 1, Issue 1, 2021, vbab011,https://doi.org/10.1093/bioadv/vbab011.BugsSubmit problems or requests to theIssue Tracker.DependenciesMandatoryHMMER 3Used for HMM profile prediction.Eddy SR, Accelerated Profile HMM Searches. PLOS Computational Biology 2011, 10.1371/journal.pcbi.1002195PftoolsUsed for PSSM prediction.Schuepbach P et al. pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. Bioinformatics 2013, 10.1093/bioinformatics/btt129LicenceGPL v3.For commercial uses please contact Dominique Koua atdominique.koua@inphb.ci.AuthorsAnicet EbouDominique Koua