{ "info": { "author": "zed.uchicago.edu", "author_email": "ishanu@uchicago.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 2.7", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Information Analysis", "Topic :: Software Development :: Libraries" ], "description": "===============\nquasinet\n===============\n\n.. figure:: https://img.shields.io/pypi/dm/quasinet.svg\n :alt: quasinet PyPI Downloads\n\n.. figure:: https://badge.fury.io/py/quasinet.svg\n :alt: ehrzero PyPI Downloads\n\n.. image:: http://zed.uchicago.edu/logo/logozed1.png\n :height: 400px\n :scale: 50 %\n :alt: alternate text\n :align: center\n\n\n.. class:: no-web no-pdf\n\n:Author: ZeD@UChicago \n:Description: Infer Non-local Structural Dependencies In Genomic Sequences. Genomic sequences are esentially compressed encodings of phenotypic information. This package provides a novel set of tools to extract long-range structural dependencies in genotypic data that define the phenotypic outcomes. The key capabilities implemented here are as follows: 1. computing the q-net given a databse of nucleic acid sequences, which is a family of conditional inference trees capturing the predictability of each nucleotide position given the rest of the genome. 2. Computing a structure-aware evolution-adaptive notion of distance between genomes, which demonstrably is much more biologically relevant compared to the standard edit distance 3. Ability to draw samples in-silico, that have a high probability of being biologically correct. For example, given a database of HIV sequences, we can generate a new genomic sequence, which has a high probability of being a valid encoding of a HIV virion. 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