cbcrg/psldoc2-nf

Name: psldoc2-nf

Owner: Notredame Lab

Description: null

Created: 2013-10-08 10:02:15.0

Updated: 2016-08-10 08:59:23.0

Pushed: 2016-08-10 08:59:21.0

Homepage: null

Size: 23822

Language: C++

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README

PSLDoc2

PSLDoc2 is the extended version of PSLDoc and it is implemented based on the nextflow framework. https://github.com/paoloditommaso/nextflow

web site: http://tcoffee.crg.cat/psldoc2

Dependencies

• PSI-BLAST (Position-Specific Initiated BLAST 2.2.28+)
• FactoMineR R package (it requires R packages: car, ellipse, lattice, cluster, scatterplot3d, leaps) http://cran.r-project.org/web/packages/FactoMineR/index.html

Configuration

Extra R libraries can be specified using the R_LIBS environment variables. Add this variable to the nextflow.config file in the project root folder, as shown in the following example:

env {
  R_LIBS = "$PWD/r_libs/"
}

Stand alone version

Prediction

1. localizaiton
   • prokaryotic : PSORTb v3 data
   • gram-negative
   • gram-positve
   • archaeal
   • eukaryotic
   • plant protein, http://cal.tongji.edu.cn/PlantLoc/
   • human
   • animal
   • fungi
   • yeast
   • Viral protein
2. nuclear
   • uclear?????(sub-localization)???????????????????sub-mitochondrian???????
     
3. protein function
   • Kinase

Build your own model

1. training phase

   • psldoc2-train.nf -> CA_train+nFoldValidation.R

   • input: model.fasta

   • output: model.tfpssm, plot_model.json, accuracy-nfold.csv, predict.csv (CA dims)

     $ nextflow psldoc2_train.nf --model=../../../data/PSL/PSORTb3.0/Archaeal.fasta --fold_num=5
     

2. predicting phase

   • psldoc2-pred.nf -> CA_pred.R (query.fasta, model.tfpssm, CA dims)

   • input: query.fasta, model.tfpssm

   • output: plot_query.json, query.pred

     $ nextflow psldoc2_pred.nf --query small.fa --model data/prokaryotic/Archaeal.tfpssm --CA_dim 36