https://github.com/widdowquinn/ncfp
Program and package that retrieves nucleotide coding sequences from NCBI that correspond to a set of input protein sequences.
https://github.com/widdowquinn/ncfp
backtranslation bioinformatics ncbi protein-to-nucleotide sequence-to-sequence uniprot
Last synced: 4 months ago
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Program and package that retrieves nucleotide coding sequences from NCBI that correspond to a set of input protein sequences.
- Host: GitHub
- URL: https://github.com/widdowquinn/ncfp
- Owner: widdowquinn
- License: mit
- Created: 2017-10-24T15:45:03.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2024-06-27T07:58:43.000Z (over 1 year ago)
- Last Synced: 2025-05-21T03:52:15.522Z (5 months ago)
- Topics: backtranslation, bioinformatics, ncbi, protein-to-nucleotide, sequence-to-sequence, uniprot
- Language: Python
- Homepage: https://widdowquinn.github.io/ncfp/
- Size: 548 KB
- Stars: 3
- Watchers: 0
- Forks: 2
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES.md
- Contributing: docs/contributing.rst
- License: LICENSE
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README
# README.md - `ncfp`
This repository contains code for a script that identifies and writes the corresponding nucleotide sequences for each protein in an input multiple sequence file to be used, for example, in backthreading coding sequences onto protein alignments for phylogenetic analyses. `ncfp` uses the NCBI accession or UniProt gene name (as appropriate) to identify source nucleotide sequences in the NCBI databases, download them, and write them to a file.
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## Quickstart: `ncfp` at the command-line
Providing an input file of protein sequences as `.fasta`, and writing output to the directory ``, while specifying a user email to NCBI of `` will generate two files: `/ncfp_aa.fasta` and `/ncfp_nt.fasta`.
```bash
ncfp .fasta
```
The file `/ncfp_aa.fasta` contains the amino acid sequences for all input proteins for which a corresponding nucleotide coding sequence could be identified, in FASTA format.
The file `/ncfp_nt.fasta` contains nucleotide coding sequences, where they could be found, for all the input proteins, in FASTA format.
Any input protein sequences for which a corresponding nucleotide sequence cannot be recovered, for any reason, are placed in the file `/skipped.fas`.
To find out more about what `ncfp` can do, try
```bash
ncfp --help
```
at the command-line
## Documentation
For more detailed information about `ncfp` as a program, or using the underlying `ncbi_cds_from_protein` Python module, please see the stable version documentation at
## License
Unless otherwise indicated, all code is licensed under the MIT license and subject to the following agreement:
(c) The James Hutton Institute 2017-2019
(c) The University of Strathclyde 2019-2024
Author: Leighton Pritchard
Contact: leighton.pritchard@strath.ac.uk
Address:
Leighton Pritchard,
Strathclyde Institute for Pharmacy and Biomedical Sciences,
Cathedral Street,
Glasgow,
G4 0RE,
Scotland,
UK
The MIT License
Copyright (c) 2017-2019 The James Hutton Institute
Copyright (c) 2019-2024 The University of Strathclyde
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.