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boctopus2 README

Dependencies:

a. hhblits executibles (version hhsuite-2.0.16) and sequence database (version uniprot20_2013_03) ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/
b. blastpgp (version blast-2.2.26) ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ 
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

SET THESE PATHS IN boctopus_main.py

Quick Usage:

python boctopus_main.py [file with fasta seqs]

python boctopus_main.py 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"

FILES:

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:

boctopus_main.py ## set paths and variables, calls boctopus_startHMM.py

boctopus_startHMM.py ## calls programs to generate sequence alignment, filter out gappy sequences, svm prediction, hmm prediction

boctopus_generatePSSM_HHblits.py ## generate sequence alignment

filter_gappyseqs.py ## filter out gappy sequences

boctopus_neighborJoin_profile_pssm.py ## create input file with PSSM values

boctopus_predictsvm.py ## svm prediction

boctopus_writepred2prf.py ## convert svm output to a profile that is used as input to HMM

boctopus_callHMM.py ## call modhmm with input profile

boctopus_parseHMMResult.py ## parse HMM output and generate text output

boctopus_getplotdata.py ## gather output data for plotting results

boctopus_makeplot.py ## plot output

SUPPLEMENTARY DATA

boctopus2_newdataset/supplementary_data/webserver_data/

ISSUES:

  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