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README.md

GprotPRED

a tool for detection and classification of G-proteins

GprotPRED is a tool for accurate detection and classification of G-proteins. It uses profile Hidden Markov Models (pHMMs) for the four known heterotrimeric Galpha protein families, the Gbeta and the Ggamma subunit in order to classify a set of protein sequences into the appropriate G-protein family. This is a standalone version of [GprotPRED] (http://aias.biol.uoa.gr/GprotPRED/) tool for offline use.

DEPENDENCIES

-hmmer software package (https://www.ebi.ac.uk/Tools/hmmer/software)
-perl

USAGE

$ GprotPRED.pl -i <input_fasta_file> -o <output_directory> -nofasta <no_fasta_output> -p <selected_profiles>

	i | input_fasta_file		Input file that contains the query protein sequences in fasta format. Required

	o | output_directory		The directory where the result output files will be stored. Required

nofasta | no_fasta_output	Use this option if you don't want fasta output. Optional, default: fasta files of the predicted proteins are generated

	p | selected_profiles		Use selected profiles only, i.e. -p Gs,Gio. Optional, default: All profiles are used (Galpha,Gs,Gio,Gq11,G1213,Gbeta,Ggamma)

EXAMPLES OF USAGE

$ GprotPRED.pl -i inFasta.fa -o ./results -p Gs,Gio

Input file: inFasta.fa
Output dir: ./results
Profiles to be run: Gs and Gio only

After the run a new directory has been created inside ./results.
The directory's name is the time-stamp of the run,
i.e. 20150910_135842, which means 10th of September 2015, 13:58:42

Inside ./results/10092015_135842 the below files are stored:
summary.txt - text summary of the results
Gs.res - hmmsearch output for Gs profile
Gio.res - hmmsearch output for Gio profile
fasta_output/Gs.fa - file that contains the proteins that match Gs profile in fasta format
fasta_output/Gio.fa - file that contains the proteins that match Gio profile in fasta format

$ GprotPRED.pl -i inFasta.fa -o ./results

Input file: inFasta.fa
Output dir: ./results
All profiles will be run by default

After the run a new directory has been created inside ./results.
The directory's name is the time-stamp of the run,
i.e. 20150910_135842, which means 10th of September 2015, 13:58:42

Inside ./results/10092015_135842 the below files are stored:
summary.txt - text summary of the results
Galpha.res - hmmsearch output for Galpha profile
Gs.res - hmmsearch output for Gs profile
Gio.res - hmmsearch output for Gio profile
Gq11.res - hmmsearch output for Gq11 profile
G1213.res - hmmsearch output for G1213 profile
Gbeta.res - hmmsearch output for Gbeta profile
Ggamma.res - hmmsearch output for Ggamma profile
fasta_output/Galpha.fa - file that contains the proteins that match Galpha profile in fasta format
fasta_output/Gs.fa - file that contains the proteins that match Gs profile in fasta format
fasta_output/Gio.fa - file that contains the proteins that match Gio profile in fasta format
fasta_output/G1213.fa - file that contains the proteins that match G1213 profile in fasta format
fasta_output/Gq11.fa - file that contains the proteins that match Gq11 profile in fasta format
fasta_output/Gbeta.fa - file that contains the proteins that match Gbeta profile in fasta format
fasta_output/Ggamma.fa - file that contains the proteins that match Ggamma profile in fasta format

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a tool for detection and classification of G-proteins

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