sequence-fairies
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: Carsten-Ke
- License: gpl-3.0
- Language: C++
- Default Branch: main
- Size: 2.47 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
Sequence-Fairies
Sequence-Fairies contains several programs that can help with your analyses.
Programs
Currently this program suite contains the following programs:
- concatenator: Concatenates alignments
- extractDomains: Can extract the domain sequences from proteins sequences
- fileMerger: Can merge sequence files into one
- isoformCleaner: Removes isoforms from a sequence set and keeps only the longest one.
- seqCheck: Can identify and solve problems with sequence files (stops and other unexpected symbols, duplicated names)
- seqExtract: Can extract sequences from files
Requirements
We try to keep the dependencies as little as possible. Current dependencies are: - cmake - boost (http://www.boost.org) - compiler with c++20 support - zlib - libbz2
You will also need the BioSeqDataLib (https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib), but this will be downloaded automatically when you run cmake
Download
bash
git clone https://zivgitlab.uni-muenster.de/domain-world/sequence-fairies.git
cd sequence-fairies
Installation
Change into the sequence-fairies directory and run the commands listed below. It will automatically download the necessary submodules, so an internet connection and git are necessary.
bash
mkdir build && cd build
cmake ..
make
Usage
Please take a look at the online manual (https://domain-world.zivgitlabpages.uni-muenster.de/sequence-fairies/) to get a detailed overview of how to run the programs.
Problems, Bugs & Suggestions
We try our best not to have any bugs in the code, unfortunately some will probably avoid us and will not be detected. If you encounter one, please be so kind and let us know. The easiest way would be to use write an email to domainworld[ at ]uni-muenster.de.
Owner
- Login: Carsten-Ke
- Kind: user
- Repositories: 1
- Profile: https://github.com/Carsten-Ke
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: Sequence-Fairies
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Carsten
family-names: Kemena-Rinke
email: c.kemena@uni-muenster.de
affiliation: University Münster
orcid: 'https://orcid.org/0000-0002-2416-9842'
identifiers:
- type: doi
value: 10.5281/zenodo.14288255
description: DOI of alls sequence-fairies versions
repository-code: >-
https://zivgitlab.uni-muenster.de/domain-world/sequence-fairies
url: >-
https://domainworld.uni-muenster.de/programs/sequence-fairies/index.html
abstract: >-
A software suite that contains a couple of small programs
to help with sequence data:
- extraction of (sub)sequences
- cleaning of isoforms
- cleaning of stop codons and other problem causing
characters
- concatenation of alignments
keywords:
- Bioinformatics
- protein sequences
- isoforms
license: GPL-3.0
GitHub Events
Total
- Release event: 3
- Delete event: 1
- Push event: 13
- Create event: 11
Last Year
- Release event: 3
- Delete event: 1
- Push event: 13
- Create event: 11
Dependencies
- actions/checkout v3 composite