micropan (version 1.0)

hmmerCleanOverlap and nonoverlap: Removing overlapping hits from HMMER3 scans

Description

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

Usage

hmmerCleanOverlap(hmmer.table)
nonoverlap(hmmer.table)

Arguments

hmmer.table

A data.frame with hmmerScan results, see readHmmer.

Value

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

Details

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 function nonoverlap is used by hmmerCleanOverlap, and not something you call directly.

The input is a data.frame of the type produced by readHmmer.

See Also

hmmerScan, readHmmer, dClust.

Examples

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