matchSeeds {microRNA} | R Documentation

## 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.

### 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.

### 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.

### Author(s)

R. Gentleman

### See Also

`seedRegions`

### Examples

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

[Package microRNA version 1.2.0 Index]