README.md

DETECT - a Density Estimation Tool for Enzyme CassificaTion

Original publication by Hung, Wasmuth, Sanford and Parkinson (2010)

DETECT implements a density estimation determination for enzyme function based on the sequence. Given a FASTA file, it produces a number of EC number predictions.

This is the python implementation that includes several optimizations compared to the original version.

Improvements mainly include lowering the nubmer of file system operations and using an SQLite database for density estimation tables.

##Examples## Sample run

python detect.py --verbose target_sequence.fasta

Running DETECT for a large sequence archive

python detect.py target_seqeunces.fasta --tabular_output --output_file predictions.tsv

Built-in help available

python detect.py --help

##Dependencies###

• NCBI BLAST
• EMBOSS suite
• SQLite3
• python2.7.3

##Required python modules##

• argparse
• sqlite3
• subprocess

pip install --install-option="--prefix=$HOME/local" [module name]

Automated install coming soon