diff --git a/README.md b/README.md index dee3c43d9d4c348cc337fce65d3c440eabf67b43..f6585d1faccde1d1d4cd3aabd4a54bc8180c3250 100644 --- a/README.md +++ b/README.md @@ -38,6 +38,11 @@ of sequences: inspired by Michael Farrar[\[3\]](#ref3). - Vectorized matrix row look-up using `permute` instructions of [AVX2](https://fr.wikipedia.org/wiki/Advanced_Vector_Extensions). +Other crates from the ecosystem provide additional features if needed: + +- [`lightmotif-tfmpvalue`](https://crates.io/crates/lightmotif-tfmpvalue) is an exact reimplementation of the TFMPvalue[\[4\]](#ref4) algorithm for converting between a score and a P-value for a given scoring matrix. +- [`lightmotif-transfac`](https://crates.io/crates/lightmotif-transfac) is a parser for position-specific scoring matrices in the [TRANSFAC](https://en.wikipedia.org/wiki/TRANSFAC) format. + *This is the Rust version, there is a [Python package](https://pypi.org/project/lightmotif) available as well.* ## 💡 Example @@ -83,7 +88,7 @@ is supported on the local platform. ## â±ï¸ Benchmarks Both benchmarks use the [MX000001](https://www.prodoric.de/matrix/MX000001.html) -motif from [PRODORIC](https://www.prodoric.de/)[\[4\]](#ref4), and the +motif from [PRODORIC](https://www.prodoric.de/)[\[5\]](#ref5), and the [complete genome](https://www.ncbi.nlm.nih.gov/nuccore/U00096) of an *Escherichia coli K12* strain. *Benchmarks were run on a [i7-10710U CPU](https://ark.intel.com/content/www/us/en/ark/products/196448/intel-core-i7-10710u-processor-12m-cache-up-to-4-70-ghz.html) running @1.10GHz, compiled with `--target-cpu=native`*. @@ -141,4 +146,5 @@ in the [Zeller team](https://github.com/zellerlab).* - <a id="ref1">\[1\]</a> Eddy, Sean R. ‘Accelerated Profile HMM Searches’. PLOS Computational Biology 7, no. 10 (20 October 2011): e1002195. [doi:10.1371/journal.pcbi.1002195](https://doi.org/10.1371/journal.pcbi.1002195). - <a id="ref2">\[2\]</a> Grant, Charles E., Timothy L. Bailey, and William Stafford Noble. ‘FIMO: Scanning for Occurrences of a given Motif’. Bioinformatics 27, no. 7 (1 April 2011): 1017–18. [doi:10.1093/bioinformatics/btr064](https://doi.org/10.1093/bioinformatics/btr064). - <a id="ref3">\[3\]</a> Farrar, Michael. ‘Striped Smith–Waterman Speeds Database Searches Six Times over Other SIMD Implementations’. Bioinformatics 23, no. 2 (15 January 2007): 156–61. [doi:10.1093/bioinformatics/btl582](https://doi.org/10.1093/bioinformatics/btl582). -- <a id="ref4">\[4\]</a> Dudek, Christian-Alexander, and Dieter Jahn. ‘PRODORIC: State-of-the-Art Database of Prokaryotic Gene Regulation’. Nucleic Acids Research 50, no. D1 (7 January 2022): D295–302. [doi:10.1093/nar/gkab1110](https://doi.org/10.1093/nar/gkab1110). +- <a id="ref4">\[4\]</a> Touzet, Hélène, and Jean-Stéphane Varré. ‘Efficient and Accurate P-Value Computation for Position Weight Matrices’. Algorithms for Molecular Biology 2, no. 1 (2007): 1–12. [doi:10.1186/1748-7188-2-15](https://doi.org/10.1186/1748-7188-2-15). +- <a id="ref5">\[5\]</a> Dudek, Christian-Alexander, and Dieter Jahn. ‘PRODORIC: State-of-the-Art Database of Prokaryotic Gene Regulation’. Nucleic Acids Research 50, no. D1 (7 January 2022): D295–302. [doi:10.1093/nar/gkab1110](https://doi.org/10.1093/nar/gkab1110). diff --git a/lightmotif-py/README.md b/lightmotif-py/README.md index 97c020db633b1a244b7029ecbd36c779a2c77819..06bc9c8960c84e58921db9d30c4c9ce47cfd9cec 100644 --- a/lightmotif-py/README.md +++ b/lightmotif-py/README.md @@ -5,6 +5,7 @@ [](https://github.com/althonos/lightmotif/actions) [](https://codecov.io/gh/althonos/lightmotif/) [](https://choosealicense.com/licenses/mit/) +[](https://lightmotif.readthedocs.io) [](https://crates.io/crates/lightmotif-py) [](https://pypi.org/project/lightmotif) [](https://pypi.org/project/lightmotif/#files) diff --git a/lightmotif-py/docs/index.rst b/lightmotif-py/docs/index.rst index 1a79ae23ccfcce225f3fdb9a0397fa6b2915468f..5c3d2ab198a84ffc420e0d760202df51812c7b14 100644 --- a/lightmotif-py/docs/index.rst +++ b/lightmotif-py/docs/index.rst @@ -11,7 +11,7 @@ LightMotif |Stars| *A lightweight* `platform-accelerated <https://en.wikipedia.org/wiki/Single_instruction,_multiple_data>`_ *library for* `biological motif <https://en.wikipedia.org/wiki/Sequence_motif>`_ *scanning using* `position weight matrices <https://en.wikipedia.org/wiki/Position_weight_matrix>`_. -|Actions| |Coverage| |License| |Crate| |PyPI| |Wheel| |Bioconda| |Python Versions| |Python Impls| |Source| |Mirror| |Issues| |Changelog| |Downloads| +|Actions| |Coverage| |License| |Docs| |Crate| |PyPI| |Wheel| |Bioconda| |Python Versions| |Python Impls| |Source| |Mirror| |Issues| |Changelog| |Downloads| .. |Actions| image:: https://img.shields.io/github/actions/workflow/status/althonos/lightmotif/python.yml?branch=main&logo=github&style=flat-square&maxAge=300 :target: https://github.com/althonos/lightmotif/actions @@ -22,6 +22,9 @@ LightMotif |Stars| .. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400 :target: https://choosealicense.com/licenses/mit/ +.. |Docs| image:: https://img.shields.io/readthedocs/lightmotif/latest?style=flat-square&maxAge=600 + :target: https://lightmotif.readthedocs.io + .. |Crate| image:: https://img.shields.io/crates/v/lightmotif-py.svg?maxAge=600&style=flat-square :target: https://crates.io/crates/lightmotif-py