| Name | na-seq JSON |
| Version |
0.3.5
JSON |
| download |
| home_page | None |
| Summary | DNA, RNA, and amino acid sequence types and functions |
| upload_time | 2025-09-01 22:01:50 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | None |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# Nucleic Acid Sequence tools
[](https://crates.io/crates/na_seq)
[](https://docs.rs/na_seq)
[](https://pypi.org/project/na-seq)
This Rust and Python library contains types and functions used for performing operations on DNA and amino acid sequences.
Its most fundamental types are the `Nucleotide` and `AminoAcid` enums, representing a single DNA nucleotide,
and single amino acid respectively. This library is general, and intended to be used by any program or library
that uses DNA sequences. It also includes an `Element` enum, with parameters associated with each element.
It includes functions to convert between `&[Nucleotide]` to string and vice-versa, and convert to and from u8
representations of the UTF-8 characters. It includes functions to serialize and deserialize in a compact binary
format, with 2 bits per nucleotide.
It includes forcefield-parameter amino acid variants, as used by Amber as the `AminoAcidProtenationVariant` enum.
Basic types impl `Display` and `ToStr`, with variants in some cases, e.g. to display an AA as a single letter,
or 3-letter string.
See [the docs](https://docs.rs/na_seq) for details on data structures and functions available.
Also includes restriction enzyme and ligation basics.
Minmal python example. See the rust docs for full details:
```python
from na_seq import *
aa = AminoAcid.from_codons([Nucleotide.A, Nucleotide.T, Nucleotide.G])
aa = AminoAcid.from_str("HIS")
aa.to_str(AaIdent.OneLetter)
aa.to_str(AaIdent.ThreeLetters)
Element.C.atomic_weight()
```
## Utility functionality
- Sequence and nucleotide complements
- Sequence and nucleotide weight
- GC content, and misc general properties of elements and amino acids. ( e.g. hydrophobicity, weight, CPK colors)
- A small restriction enzyme library
We may add Sequence searches, and other utility features in the future.
This library is used by the [PlasCAD](https://github.com/David-OConnor/plascad) plasmid editor and [Daedalus](https://github.com/David-OConnor/daedalus)
molecule viewer.
Note: The Python version currently does not include restriction-enzyme and ligation functionality.
Raw data
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"description": "# Nucleic Acid Sequence tools\n\n[](https://crates.io/crates/na_seq)\n[](https://docs.rs/na_seq)\n[](https://pypi.org/project/na-seq)\n\nThis Rust and Python library contains types and functions used for performing operations on DNA and amino acid sequences. \nIts most fundamental types are the `Nucleotide` and `AminoAcid` enums, representing a single DNA nucleotide, \nand single amino acid respectively. This library is general, and intended to be used by any program or library \nthat uses DNA sequences. It also includes an `Element` enum, with parameters associated with each element.\n\nIt includes functions to convert between `&[Nucleotide]` to string and vice-versa, and convert to and from u8 \nrepresentations of the UTF-8 characters. It includes functions to serialize and deserialize in a compact binary\nformat, with 2 bits per nucleotide.\n\nIt includes forcefield-parameter amino acid variants, as used by Amber as the `AminoAcidProtenationVariant` enum.\n\nBasic types impl `Display` and `ToStr`, with variants in some cases, e.g. to display an AA as a single letter,\nor 3-letter string.\n\nSee [the docs](https://docs.rs/na_seq) for details on data structures and functions available.\n\nAlso includes restriction enzyme and ligation basics.\n\nMinmal python example. See the rust docs for full details:\n\n```python\nfrom na_seq import *\n\naa = AminoAcid.from_codons([Nucleotide.A, Nucleotide.T, Nucleotide.G])\naa = AminoAcid.from_str(\"HIS\")\n\naa.to_str(AaIdent.OneLetter)\naa.to_str(AaIdent.ThreeLetters)\n\nElement.C.atomic_weight()\n```\n\n\n## Utility functionality\n- Sequence and nucleotide complements\n- Sequence and nucleotide weight\n- GC content, and misc general properties of elements and amino acids. ( e.g. hydrophobicity, weight, CPK colors)\n- A small restriction enzyme library\n\n\nWe may add Sequence searches, and other utility features in the future.\n\nThis library is used by the [PlasCAD](https://github.com/David-OConnor/plascad) plasmid editor and [Daedalus](https://github.com/David-OConnor/daedalus) \nmolecule viewer.\n\nNote: The Python version currently does not include restriction-enzyme and ligation functionality.\n",
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