lorfs: Longest ORF

In microseq: Basic Biological Sequence Handling

Longest ORF

Description

Filtering an orf.table with ORF information to keep only the LORFs.

Usage

lorfs(orf.tbl)

Arguments

orf.tbl

A tibble with the nine columns of the GFF-format (see findOrfs).

Details

For every stop-codon there are usually multiple possible start-codons in the same reading frame (nested ORFs). The LORF (Longest ORF) is defined as the longest of these nested ORFs, i.e. the ORF starting at the most upstream start-codon matching the stop-codon.

Value

A tibble with a subset of the rows of the argument orf.tbl. After this filtering the Type variable in orf.tbl is changed to "LORF". If you want to retrieve the LORF sequences, use gff2fasta.

Author(s)

Lars Snipen and Kristian Hovde Liland.

See Also

readGFF, findOrfs, gff2fasta.

Examples

# See the example in the Help-file for findOrfs.

microseq documentation built on Aug. 21, 2023, 5:10 p.m.