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Martin Larralde
LightMotif
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5068087c
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5068087c
authored
6 months ago
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Martin Larralde
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Display link to stable documentation in Python `README.md` [ci skip]
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@@ -5,7 +5,7 @@
[

](https://github.com/althonos/lightmotif/actions)
[

](https://codecov.io/gh/althonos/lightmotif/)
[

](https://choosealicense.com/licenses/mit/)
[

](https://lightmotif.readthedocs.io)
[

](https://lightmotif.readthedocs.io
/en/stable/
)
[

](https://crates.io/crates/lightmotif-py)
[

](https://pypi.org/project/lightmotif)
[

](https://pypi.org/project/lightmotif/#files)
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.. |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
.. |Docs| image:: https://img.shields.io/readthedocs/lightmotif/
stable
?style=flat-square&maxAge=600
:target: https://lightmotif.readthedocs.io
/en/stable/
.. |Crate| image:: https://img.shields.io/crates/v/lightmotif-py.svg?maxAge=600&style=flat-square
:target: https://crates.io/crates/lightmotif-py
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@@ -90,10 +90,29 @@ searches for a motif encoded in a position weight matrix. The position
scanning combines several techniques to allow high-throughput processing
of sequences:
- Compile-time definition of alphabets and matrix dimensions.
- Sequence symbol encoding for fast table look-ups, as implemented in HMMER or MEME
- Striped sequence matrices to process several positions in parallel, inspired by Michael Farrar.
- Vectorized matrix row look-up using ``permute`` instructions of `AVX2 <https://fr.wikipedia.org/wiki/Advanced_Vector_Extensions>`_.
.. grid:: 1 2 4 4
:gutter: 1
.. grid-item-card:: :fas:`fa-solid fa-arrow-down-a-z` Constant alphabets
Compile-time definition of alphabets and matrix dimensions, allowing
constant pointer incrementation in loops over strided arrays.
.. grid-item-card:: :fas:`fa-solid fa-arrow-down-1-9` Ordinal encoding
Sequence symbol encoding as indices fo fast table look-ups, as
implemented in `HMMER <https://hmmer.org>`_ or
`MEME <https://meme-suite.org/>`_.
.. grid-item-card:: :fas:`fa-solid fa-table` Striped matrices
Striped sequence matrices for parallel processing,
inspired by Michael Farrar (:pmid:`17110365`).
.. grid-item-card:: :fas:`fa-solid fa-microchip` Platform code
Vectorized matrix-row look-up using ``permute`` instructions of
`AVX2 <https://fr.wikipedia.org/wiki/Advanced_Vector_Extensions>`_.
*This is the Python version, there is a* `Rust crate <https://docs.rs/lightmotif>`_ *available as well.*
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