.. peptides documentation master file, created by sphinx-quickstart on Sat Oct 23 18:17:35 2021. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. `peptides.py` |stars| ===================== .. |Stars| image:: https://img.shields.io/github/stars/althonos/peptides.py.svg?style=social&maxAge=3600&label=Star :target: https://github.com/althonos/peptides.py/stargazers *Physicochemical properties, indices and descriptors for amino-acid sequences.* |Actions| |Coverage| |License| |PyPI| |Bioconda| |Wheel| |Versions| |Implementations| |Source| |Mirror| |Issues| |Docs| |Changelog| |Downloads| .. |Actions| image:: https://img.shields.io/github/actions/workflow/status/althonos/peptides.py/test.yml?branch=main&logo=github&style=flat-square&maxAge=300 :target: https://github.com/althonos/peptides.py/actions .. |Coverage| image:: https://img.shields.io/codecov/c/gh/althonos/peptides.py?style=flat-square&maxAge=600 :target: https://codecov.io/gh/althonos/peptides.py/ .. |PyPI| image:: https://img.shields.io/pypi/v/peptides.svg?style=flat-square&maxAge=3600 :target: https://pypi.python.org/pypi/peptides .. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/peptides?style=flat-square&maxAge=3600&logo=anaconda :target: https://anaconda.org/bioconda/peptides .. |Wheel| image:: https://img.shields.io/pypi/wheel/peptides?style=flat-square&maxAge=3600 :target: https://pypi.org/project/peptides/#files .. |Versions| image:: https://img.shields.io/pypi/pyversions/peptides.svg?style=flat-square&maxAge=3600 :target: https://pypi.org/project/peptides/#files .. |Implementations| image:: https://img.shields.io/badge/impl-universal-success.svg?style=flat-square&maxAge=3600&label=impl :target: https://pypi.org/project/peptides/#files .. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg?style=flat-square&maxAge=3600 :target: https://choosealicense.com/licenses/gpl-3.0/ .. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square :target: https://github.com/althonos/peptides.py/ .. |Mirror| image:: https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square&maxAge=2678400 :target: https://git.embl.de/larralde/peptides.py/ .. |Issues| image:: https://img.shields.io/github/issues/althonos/peptides.py.svg?style=flat-square&maxAge=600 :target: https://github.com/althonos/peptides.py/issues .. |Docs| image:: https://img.shields.io/readthedocs/peptides?style=flat-square&maxAge=3600 :target: http://peptides.readthedocs.io/en/stable/?badge=stable .. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square :target: https://github.com/althonos/peptides.py/blob/main/CHANGELOG.md .. |Downloads| image:: https://img.shields.io/pypi/dm/peptides?style=flat-square&color=303f9f&maxAge=86400&label=downloads :target: https://pepy.tech/project/peptides Overview -------- ``peptides.py`` is a pure-Python package to compute common descriptors for protein sequences. It started as a port of `Peptides `_, the R package written by `Daniel Osorio `_ for the same purpose, but now also provides some more features from `EMBOSS `_, `ExPASy Protein Identification and Analysis Tools `_, and `Rcpi `_. This library has no external dependency and is available for all modern Python versions (3.6+). A non-exhaustive list of available features: - Amino-acid Statistics: - Number of occurrences in the peptide sequence - Frequency in the peptide sequence - `QSAR `_ descriptors: - `BLOSUM indices `_ - `Cruciani properties `_ - `FASGAI vectors `_ - `Kidera factors `_ - `Atchley factors `_ - `MS-WHIM scores `_ - `PCP descriptors `_ - `ProtFP descriptors `_ - `Sneath vectors `_ - `ST-scales `_ - `SVGER descriptors `_ - `T-scales `_ - `VHSE-scales `_ - `Z-scales `_ - Sequence profiles: - Hydrophobicity profile using one of 39 proposed scales. - Hydrophobic moment profile based on `Eisenberg, Weiss and Terwilliger (1984) `_. - Membrane position based on `Eisenberg (1984) `_. - Physical-chemical properties: - Aliphatic index proposed in `Ikai (1980) `_. - Instability index proposed in `Boman (2003) `_. - Theoretical net charge based on the `Henderson-Hasselbach equation `_. - Isoelectric point using one of 8 pKa scales. - Molecular weight, taking into account isotope labelling, using one of 3 average weight tables. - Biological properties: - Structural class using methods and reference data from either `Nakashima, Nishikawa & Ooi (1985) `_, `Chou (1989) `_, `Chou & Zhang (1992) `_, or `Chou, Liu, Maggiora & Zhang (1998) `_. Setup ----- ``peptides`` is a pure Python package available for all modern Python (3.6+). Run ``pip install peptides`` in a shell to download the latest release, or have a look at the :doc:`Installation page ` to find other ways to install ``peptides.py``. Library ------- .. toctree:: :maxdepth: 2 User Guide API Reference Related Projects ---------------- The following Python libraries may be of interest for bioinformaticians. .. grid:: 1 3 5 5 :gutter: 1 .. grid-item-card:: :fas:`diamond` PyHMMER :link: https://pyhmmer.readthedocs.io Profile Hidden Markov Models (with HMMER). .. grid-item-card:: :fas:`fire` Pyrodigal :link: https://pyrodigal.readthedocs.io Prokaryotic Gene Finding (with Prodigal). .. grid-item-card:: :fas:`virus-covid` Pyrodigal-gv :link: https://github.com/althonos/pyrodigal-gv Pyrodigal for Giant Viruses. .. grid-item-card:: :fas:`align-center` PyFAMSA :link: https://pyfamsa.readthedocs.io Multiple Sequence Alignment (with FAMSA). .. grid-item-card:: :fas:`scissors` PytrimAl :link: https://pytrimal.readthedocs.io Alignment Trimming (with trimAl). .. grid-item-card:: :fas:`music` LightMotif :link: https://lightmotif.readthedocs.io Platform-accelerated motif scoring. .. grid-item-card:: :fas:`knife;fa-custom` Diced :link: https://diced.readthedocs.io CRISPR Detection (with MinCED). .. grid-item-card:: :fas:`table-cells` Scoring Matrices :link: https://scoring-matrices.readthedocs.io Scoring matrices for Cython. .. grid-item-card:: :fas:`chain` Pyskani :link: https://pyskani.readthedocs.io Average Nucleotide Identity (with skani). .. grid-item-card:: :fas:`forward-fast` PyFastANI :link: https://pyfastani.readthedocs.io Average Nucleotide Identity (with FastANI). .. grid-item-card:: :fas:`magnifying-glass` PyJess :link: https://pyjess.readthedocs.io Geometric Template Matching (with Jess). .. grid-item-card:: :fas:`repeat` PyTantan :link: https://pytantan.readthedocs.io Tandem Repeat Masking (with Tantan). .. grid-item-card:: :fas:`gem` PyOpal :link: https://pyopal.readthedocs.io Query/Database Aligner (with Opal). .. grid-item-card:: :fas:`sword;fa-custom` PySWRD :link: https://pyswrd.readthedocs.io Database Heuristic Filtering (with SWORD). .. grid-item-card:: :fas:`rocket` Mini3di :link: https://github.com/althonos/mini3di Protein structure to 3di in pure Python. .. grid-item-card:: :fas:`calculator` ``peptides.py`` :link: https://peptides.readthedocs.io Peptide descriptors for Python. .. grid-item-card:: :fas:`diagram-project` Pronto :link: https://pronto.readthedocs.io Open Biomedical Ontologies for Python. .. grid-item-card:: :fas:`box` NAFcodec :link: https://nafcodec.readthedocs.io Nucleotide Archival Format for Python. .. grid-item-card:: :fas:`bank` ``gb-io.py`` :link: https://gb-io.readthedocs.io Fast GenBank parser for Python (with ``gb-io``). License ------- This library is provided under the `GNU General Public License v3.0 `_. The original R `Peptides` package was written by `Daniel Osorio `_, `Paola Rondón-Villarreal `_ and `Rodrigo Torres `_, and is licensed under the terms of the `GNU General Public License v2.0 `_. The `EMBOSS `_ applications are released under the `GNU General Public License v1.0 `_. *This project is in no way not affiliated, sponsored, or otherwise endorsed by the original* `Peptides`_ *authors. It was developed by* `Martin Larralde `_ *during his PhD project at the* `European Molecular Biology Laboratory `_ *in the* `Zeller team `_.