Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary
Repository
Alignment of miRNA sequences
Basic Info
- Host: GitHub
- Owner: molinerisLab
- License: agpl-3.0
- Language: Python
- Default Branch: main
- Size: 70.3 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
miRAl
Optimized tool to perform the Needleman-Wunsch algorithm to align mature miRNA sequences.
Installation using conda:
conda install -c molinerislab miRAl
Description:
Needleman-Wunsch alignment of mature miRNAs with tje possibility to weight differently the nucleotides in the miRNA seed. The tool can also return a FASTA file with the alignment in addition to the file with the Needleman-Wunsch scores.
Usage and options:
``` Usage: miRAl [OPTIONS] fasta.fa [fasta2.fa] < couples.tsv >output.tsv
Options: -h, --help show the help message and exit -t STRING, --seed-type=STRING Specify the format of the seed you want to consider (default: 6mer). Options are: 6mer, 7mer, 8mer or null -g INT, --gap-open=INT Specify the gap opening penalty (default: -5) -e INT, --gap-extend=INT Specify the gap extension penalty (default: -4) -x INT, --mismatch-score=INT Specify the mismatch score (default: -1) -m INT, --match-score=INT Specify the match score (default: 1) -y INT, --seed-mismatch-score=INT Specify the seed mismatch score (default: -3) -n INT, --seed-match-score=INT Specify the seed match score (default: 3) -p, --penalize-end-gaps Penalize end gaps (default: False) -o, --one-alignment Return only one alignment per pair (default: False) -s, --score-only Return only the alignment score (default: False) -f -a, --fasta-out Change the output format. Produce a simil-fasta format, where the header contains the names of the two aligned sequences while the "body" contains the alignment score (absolute and normalized) and the ```
The different types of seed can be visualized as follows:
The additional output FASTA file with the alignment, is composed of blocks like the following one:
Owner
- Name: molinerisLab
- Login: molinerisLab
- Kind: organization
- Location: Italy
- Repositories: 2
- Profile: https://github.com/molinerisLab
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Agasso
given-names: Leonardo
- family-names: Caselle
given-names: Michele
orcid: https://orcid.org/0000-0001-5488-142X
- family-names: Molineris
given-names: Ivan
orcid: https://orcid.org/0000-0003-2102-0804
title: "Align miRNA sequence more carefully with miRAl"
version: 0.1.1
identifiers:
- type: doi
value: 10.5281/zenodo.13683070
date-released: 2024-09-04