microRNA (version 1.30.0)

matchSeeds: A function to match seed regions to sequences.

Description

Given an input set of seed regions and a set of sequences all locations of the seed regions (exact matches) within the sequences are found.

Usage

matchSeeds(seeds, seqs)

Arguments

seeds

The seeds, or short sequences, to match.

seqs

The sequences to find matches in.

Value

A list containing one entry for each element of seeds that had at least one match in one entry of seqs. Each element of this list is a named vector containing the elements of seqs that the corresponding seed has an exact match in.

Details

We presume that the problem is an exact matching problem and that all sequences are in the correct orientation for that. If, for example, you start with seed regions from a microRNA (for seeds) and 3'UTR sequences (for seqs), then you would want to reverse complement one of the two sequences. And make sure all sequences are either DNA or RNA.

Names from either seeds or seqs are propogated, as much as is possible.

See Also

seedRegions

Examples

library(Biostrings)
data(hsSeqs)
data(s3utr)
hSeedReg = seedRegions(hsSeqs)
comphSeed = as.character(reverseComplement(RNAStringSet(hSeedReg)))
comph = RNA2DNA(comphSeed)
mx = matchSeeds(comph, s3utr)

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