Miniprot

Miniprot aligns protein sequences to genomic DNA to recover spliced,

API

Miniprot aligns protein sequences to genomic DNA to recover spliced, protein-to-genome alignments useful for gene annotation. The Miniprot workflow is used to generate a GTF file from protein-to-genome alignments. The workflow consists of the following steps: 1. Index the masked genome using Miniprot. 2. Align the protein dataset to the indexed genome using Miniprot.

References

[13]

ensembl.tools.anno.protein_annotation.miniprot.run_miniprot(masked_genome, output_dir, protein_dataset, miniprot_bin=PosixPath('miniprot'), num_threads=1, top_n=1, outs=1.0, protein_set='uniprot')

Run Miniprot protein-to-genome alignment workflow.

Parameters:

• masked_genome (Path)

• output_dir (Path)

• protein_dataset (Path)

• miniprot_bin (Path)

• num_threads (int)

• top_n (int)

• outs (float)

• protein_set (str)

Return type:

None