Code and data for the SIEVE-Ub prediction algorithm for prediction of E3 ubiquitin ligase mimics
Accompanies the preprint: https://peerj.com/preprints/27292/
Published paper: https://peerj.com/articles/7055/
Files:
KmerFeatures.py : Python code that transforms a protein fasta file into kmer features suitable for use
with. the SIEVEUb.R code.
SIEVEUb.R : R code to train and validate models based on kmer features. Includes code for family-wise
cross-validation and family-wise scoring of overrepresented kmers.
SIEVEUbApply.R : an R script that allows reading in a set of features output from KmerFeatures and applying
the predictive model from the paper to output predictions for each protein.
SIEVEUbCode.Rmd : RMarkdown file for doing the analysis described in the paper. This RMarkdown has code for
regenerating most of the figures, tables, and supplemental figures and tables from the paper.
make_prediction.csh : shell script that will provide predictions of ubiquitin ligase given an input fasta file.
data/1032069.3.PATRIC.faa : example PATRIC genome fasta file from a single genome
data/FamiliesConservative.txt : list of example proteins used for positive and negative examples, their annotations,
and identified sequence families
data/PATRIC.genomes : list of genomes from PATRIC used in the paper
data/PATRIC_secretion_systems.txt : Type III, IV, and VI secretion system components identified in each PATRIC genome used
data/SIEVEUb_best_model.Rdata : Rdata file containing the best Ub ligase model
data/SIEVEUb_minimal_model.Rdata : Rdata file containing the minimal Ub. ligase model with 10 features
data/best_model_1280features.txt : list of features included in the best Ub ligase predictive model
data/legionella_examples.fasta : FASTA protein sequence for newly discovered UUb ligase RavN
data/legionella_examples_k14red0_minimal10.txt : feature file for RavN using the minimal model identified
data/minimal_model_10features.txt : kmers contained in the 10 kmer minimal model
data/patric_ubligase_predictions_best_model.txt.gz : predictions for the PATRIC subset used in the paper with the best
Ub ligase predictive model
data/ubligase_examples_ids.fasta : FASTA file containing protein sequences of positive and negative examples used in this
study. Please see FamiliesConservative.txt for information about these sequences.
data/ubligase_examples_ids_minimal_model_10features.html : HTML file that lists the examples used in this study and where
the top 10 most predictive kmers map to the sequences.
data/ubligase_examples_ids_minimal_model_10features.tab : List of most predictive 10 kmers locations in each of the examples
used in the study.
data/uniprot_search.readme : short description of Uniprot search and filtering process used to identify positive
examples for E3 ubiquitin ligase
data/red0/ : features for reduced alphabet 0 over a range of kmer lengths from 3-20
data/rnd0/ : features for randomized binary alphabets
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