hmmerCleanOverlap: Removing overlapping hits from HMMER3 scans
In micropan: Microbial Pan-Genome Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Removing hits to avoid overlapping HMMs on the same protein sequence.

1	hmmerCleanOverlap(hmmer.tbl)

hmmer.tbl

A table (tibble) with hmmerScan results, see readHmmer.

When scanning sequences against a profile HMM database using hmmerScan, we often find that several patterns (HMMs) match in the same region of the query sequence, i.e. we have overlapping hits. The function hmmerCleanOverlap will remove the poorest overlapping hit in a recursive way such that all overlaps are eliminated.

The input is a tibble of the type produced by readHmmer.

A tibble which is a subset of the input, where some rows may have been deleted to avoid overlapping hits.

Lars Snipen and Kristian Hovde Liland.

hmmerScan, readHmmer, dClust.