bifrost

require(GCModeller); #' Bifrost: the gene prediction toolkit imports "bifrost" from "seqtoolkit";

Bifrost: the gene prediction toolkit

This R# package module provides the api for run gene prediction on the genomics contigs assembly sequence:

prodigal: the ab-initio prokaryotic gene prediction algorithm (PROkaryotic DYnamic programming Gene-finding ALgorithm), works on the prokaryotic MAGs contigs assembly sequence;

metaeuk: the homology based eukaryotic gene prediction algorithm, works on the eukaryotic contigs assembly sequence with a given reference protein database;

The gene prediction result of the prodigal algorithm is a collection of the PredictionResult object, which could be exported as:

GFF3 table via the as.gff3 api;

nucleotide/protein fasta sequence via the as.genes/as.proteins api;

a score table data frame via the as.data.frame api, for save as a csv file by the write.csv api.

.NET clr type export
prodigal: TrainingModel	训练模型 - 包含编码区模型、RBS模型、起始密码子模型
metaeuk_config: MetaEukConfig

.NET clr function exports
as.data.frame.predictionresult	PredictionResult: 基因预测结果
prodigal_training	Train the gene prediction model in an unsupervised manner
prodigal	Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm)
metaeuk	MetaEuk: the homology based eukaryotic gene prediction
as.gff3	cast the gene prediction result as GFF3 table format
as.proteins	Extract the protein sequences from the gene prediction result, and return as FASTA format. The sequence ID is in the format of "seqid_geneindex". For example, "contig1_5" means the 5th predicted gene on contig1. The sequence description is in the format of "start-end(strand)". For example, "100-900(+)" means the gene starts at position 100, ends at position 900, and is on the forward strand.
as.genes	Extract the gene sequences from the gene prediction result, and return as FASTA format. The sequence ID is in the format of "seqid_geneindex". For example, "contig1_5" means the 5th predicted gene on contig1. The sequence description is in the format of "start-end(strand)". For example, "100-900(+)" means the gene starts at position 100, ends at position 900, and is on the forward strand.

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