orfipy
pyrodigal
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orfipy | pyrodigal | |
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2 | 1 | |
46 | 122 | |
- | - | |
1.8 | 8.7 | |
over 2 years ago | 12 days ago | |
Python | Cython | |
MIT License | GNU General Public License v3.0 only |
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orfipy
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Looking for a tool to convert a whole fasta file with CDS sequences to a fasta file with protein sequences.
You can probably use or adapt https://github.com/urmi-21/orfipy. I've never used this but it looks fantastic.
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Question about ORF finder
You don't need any specific hardware to run most bioinformatics programs. There is a web application of ORF finder and if you want to run large amounts of analyses you probably want to run them in a Linux environment. Look at Windows Subsystem for Linux if you are a Windows user. You may also be interested in new ORF finders like this one: https://github.com/urmi-21/orfipy
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?
galaxy - Data intensive science for everyone.
Prodigal - Prodigal Gene Prediction Software
Biopython - Official git repository for Biopython (originally converted from CVS)
cyvcf2 - cython + htslib == fast VCF and BCF processing
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database
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.
pybase64 - Fast Base64 encoding/decoding in Python
DNA-to-Amino-Acid-Converter - This program breaks apart a DNA string and dispalys each amino acid associated with each codon
masurca