boctopus2 README


a. hhblits executibles (version hhsuite-2.0.16) and sequence database (version uniprot20_2013_03)
b. blastpgp (version blast-2.2.26) 
c. modhmm (executible provided in this folder modhmm/)
    d. R needs "e1071" library. In R, type install.packages("e1071")
    e. install.packages("optparse") for passing arguments to R


Quick Usage:

python [file with fasta seqs]

python LPTD.fasta

WORKING EXAMPLES with input, intermediate results and output:

A5VZA8_PSEP1.fasta AIDA.fasta ESPP_ECO57.fasta ESTA.fasta LAMB.fasta LPTD.fasta PA1_ECOLI.fasta Q5F5W8_NEIG1.fasta Q8D0Z7_YERPE.fasta INVA.fasta

Output description:

output folder = "output/"

a. Predicted topology "[pname]_ioIOS.prf.txt_stateName.txt"
I=inner loop
O=outer loop
i=pore-facing residue in a membrane strand
o=lipid-facing residue in a membrane strand

b. Image of predicted topology "[pname]_ioIOS.prf.txt_svm_topo.png"
c. HMM path travesered "[pname]_ioIOS.prf.txt_statepath.txt"
d. HHblits output "[pname].hhr"


SVM: objects trained on the dataset with window sizes estimated using a cross-validation test. svmtrain42_innerloop.Rdata svmtrain42_lipidfacing.Rdata svmtrain42_outerloop.Rdata svmtrain42_porefacing.Rdata

R scripts (for SVM-stage predictions):

traninedsvmRadial_cyto.R traninedsvmRadial_extra.R traninedsvmRadial_lipid.R traninedsvmRadial_pore.R

HMM: architecture and parameters st911_Noss.hmg

Python scripts: ## set paths and variables, calls ## calls programs to generate sequence alignment, filter out gappy sequences, svm prediction, hmm prediction ## generate sequence alignment ## filter out gappy sequences ## create input file with PSSM values ## svm prediction ## convert svm output to a profile that is used as input to HMM ## call modhmm with input profile ## parse HMM output and generate text output ## gather output data for plotting results ## plot output




  1. The header of input fasta file can not have spaces. handle it correctly.

Who do I talk to?

  • Repo owner or admin: Sikander Hayat and Arne Elofsson
  • Other community or team contact: xxx