Prodigal
pyrodigal
Prodigal | pyrodigal | |
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4 | 1 | |
410 | 122 | |
- | - | |
0.0 | 8.7 | |
4 months ago | 2 days ago | |
C | Cython | |
GNU General Public License v3.0 only | GNU General Public License v3.0 only |
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Prodigal
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DNA to amino acid sequence?
use prodigal https://github.com/hyattpd/prodigal
- Trying to Install Prodigal from GitHub
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ORF prediction for non-model organism with DNA sequence only
I'd use prodigial and not their ugly closed source software...
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How do I convert a scaffold into genes?
Prodigal is a commonly used gene-caller for prokaryotic genomes. In fact, I believe it is used by Prokka, as mentioned by another commenter.
pyrodigal
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DNA to amino acid sequence?
True! I believe bakta relies on this python implementation of prodigal for translation https://github.com/althonos/pyrodigal
What are some alternatives?
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
cyvcf2 - cython + htslib == fast VCF and BCF processing
BRAKER - BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
MultiQC - Aggregate results from bioinformatics analyses across many samples into a single report.
DNA-to-Protein-sequence - Translate a string containing a nucleotide sequence(DNA) into a string containing the corresponding sequence of amino acids.
orfipy - Fast and flexible ORF finder
DNA-to-Amino-Acid-Converter - This program breaks apart a DNA string and dispalys each amino acid associated with each codon
pybase64 - Fast Base64 encoding/decoding in Python
masurca