GitHub - gkrieg/Nnessy: Tool for protein secondary structure prediction that avoids database homology search

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Tool for protein secondary structure prediction that avoids database homology search

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Name		Name	Last commit message	Last commit date
Latest commit History 47 Commits
datasets		datasets
dfs		dfs
logs		logs
src		src
templatedatabases		templatedatabases
trees		trees
weights		weights
LICENSE		LICENSE
README.txt		README.txt
accuracyestimator.py		accuracyestimator.py
alpha.words.zip		alpha.words.zip
beta.words.zip		beta.words.zip
convertprobabilities.py		convertprobabilities.py
dynamicprogramming.py		dynamicprogramming.py
eightoverlappingwords.py		eightoverlappingwords.py
example.fasta		example.fasta
getSecondaryStructure.py		getSecondaryStructure.py
identstitch.py		identstitch.py
install		install
newgreedy.py		newgreedy.py
nnessy		nnessy
other.words.zip		other.words.zip
overlappingwords.py		overlappingwords.py
segment1		segment1
segment2		segment2
segment3		segment3
segment4		segment4
segment5		segment5
segment6		segment6
segment7		segment7
segment8		segment8
segment9		segment9
split.py		split.py
splitfile.py		splitfile.py
transitions.txt		transitions.txt
transitions8.txt		transitions8.txt
weights.txt		weights.txt

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To install Nnessy, run:

./install


To run Nnessy, make sure that your input file is in .fasta format and contains a single sequence


./nnessy -i [input].fasta [-n numthreads] [-o output]


If no output file is specified, the secondary structure will be placed in a file with the name output/[input].ss, which has the secondary structure.

-n option allows the number of threads to be specified if run in a parallel setting.