prokka
Prodigal
prokka | Prodigal | |
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5 | 4 | |
754 | 404 | |
- | - | |
0.0 | 0.0 | |
23 days ago | 3 months ago | |
Perl | C | |
- | GNU General Public License v3.0 only |
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prokka
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orfs in DNA
If you need more accurate ORF(CDS) prediction including functional annotation, I recommend using CLI tools such as prokka, bakta, or DFAST (DFAST is also available in a web version).
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Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
reCOGnizer (https://github.com/iquasere/reCOGnizer) can annotate with COGs, and the other databases available at CDD. It obtains all information concerning COGs description and categories, and outputs krona plots and TSV tables in formats easy to analyze. There is also mantis (https://github.com/PedroMTQ/mantis), prokka (https://github.com/tseemann/prokka) and DFAST (https://github.com/nigyta/dfast_core), the latter two work on contigs and the first two are for proteins
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ORF prediction for non-model organism with DNA sequence only
I just checked out Prokka, which uses Prodigal to predict genes. They do not seem to have any reservations for viruses. Thus, I recommend using Prokka directly, since that will conveniently add functional annotations.
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Genome analysis cost
If you do DNA sequencing and receive the sequencing files as fastq files (normal from sequencing) then spades to assemble the genome, then put it through PROKKA to annotate it. Here's a beginners guide, the most difficult part is downloading the programs onto your laptop.
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.
What are some alternatives?
spades - SPAdes Genome Assembler
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
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
dfast_core - DDBJ Fast Annotation and Submission Tool
DNA-to-Protein-sequence - Translate a string containing a nucleotide sequence(DNA) into a string containing the corresponding sequence of amino acids.
DNA-to-Amino-Acid-Converter - This program breaks apart a DNA string and dispalys each amino acid associated with each codon
funannotate - Eukaryotic Genome Annotation Pipeline
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database
mantis - A package to annotate protein sequences