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OSTIR Documentation

OSTIR is a Python package for predicting the rates at which ribosomes will bind to and initiate translation from different start codons in bacterial mRNAs. It uses the ViennaRNA software suite to perform the necessary free energy calculations. The code builds on the last open source version of the RBS calculator that implements the calculations described in Salis 2009.

OSTIR includes several improvements in usability. It supports multi-FASTA input with command line parameters or CSV input that can define parameters on a per-sequence basis. Additionally, OSTIR supports multi-threaded execution, accelerating use cases that require the analysis of very large sequences.

Background

Explains the thermodynamic model and shows typical results for E. coli genes.

Installation

Methods that are available for installing OSTIR and its dependencies.

Command Line Usage

How to run OSTIR at the command line with an explanation of input and output file formats.

Python Module Usage

How to call OSTIR as a Python function with an explanation of parameters and return values.

Developer Information

How you can contribute to improving OSTIR.