nanjiang/boctopus2 repository overview

⁠BOCTOPUS2

A predictor for transmembrane beta-barrel topology

⁠Authors

Sikander Hayat Arne elofsson Christoph Peters Nanjiang Shu Konstantinos D. Tsirigos

⁠Note

The original bitbucket repo https://bitbucket.org/sikander_hayat/boctopus2_newdataset⁠ does not exist any more. The source code has been moved to this GitHub repo.

⁠Requirements

1. Softwares

• Python 2.7+ (But not Python 3)
• HHBLITS executibles (version hhsuite-2.0.16)
• blastpgp (blast-2.2.26) ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
• R libraries e1071 and optparse

1. Database HHblits sequence database (version uniprot20_2013_03) ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/

⁠Before usage

⁠Quick Usage

python src/boctopus_main.py SEQFLE OUTPATH

⁠Description of the output files

1. query_topologies.txt: predicted topology

   Explanation of symbols.

   • I: inner loop
   • O: outer loop
   • i: pore-facing residue in a membrane strand
   • o: lipid-facing residue in a membrane strand

2. query.predict.png: visual illustration of the predicted topology

3. profile.txt: HMM profile of the sequence to be predicted

4. pssm.txt: position specific substitution matrix generated by PSI-BLAST

5. quer.fa: a copy of the sequence to be predicted