DPRED 1.0.4

DPRED is a softwares package for HMM domain prediction and validation

=============================================================================== This is an implementation for automatic HMM-based domain prediction and k-fold cross-validation, in Python. The program still needs some optimization, and it will require more or less 7 minutes to finish. It uses mTM-align and HMMER packages, for which you can find the references here.

REQUIREMENTS: HMMER and BioPython have to be installed. Also, check for your Python built-in modules availability in the distribution depository.

DISCLAIMER: Permission is granted to use, copy, modify, and distribute this program for any purpose, with or without fee, provided that the notices in the header, reference information, and this copyright notice are included in all copies or substantial portions of the software. The software is provided "as is," without any express or implied warranty.

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========================= How to install DPRED

pip install DPRED

You can find further informations at: https://pypi.org/project/DPRED/

===================== How to use DPRED

Usage: dpred --pfam -k -l

-k K The number of folds to on which to base the cross-validation procedure

-l range The domain lenght range. Has to be specified with a ":", e.g. 50:80

-n name The domain's name. It will be written in the .hmm and .txt valdidation files. Default is "domain"

--res resolution The maximum resolution of PDB structures on which to base the HMM generation

--mut mutation count The mutation count per pdb structure. Default is 0

--iden identity The percentage of sequence identity used for grouping pdb entities. Default is 50

--bid blast identity The percentage of sequence identity used for positives blast selection. Default is 95.

--mtm msa directory Keep the MSA directory. Default is False.

--msa msa file Keep the MSA directory. Default is False.

--pdb PDB directory Keep the PDB structures directory. Default is False.

--chunks chunks directory Keep the chunks directory generated during the cross-validation procedure. Default is False.

--sets sets directory Keep the sets directory generated during the cross-validation procedure. Default is False.

--db blast database directory Keep the blast database directory. Default is False.