findORFsFasta {ORFik} | R Documentation

## Finds Open Reading Frames in fasta files.

### Description

Searches through each fasta header and reports all ORFs found for sense (+) and antisense strand (-) in all frames. Name of the header will be used as seqnames of reported ORFs. Each fasta header is treated separately, and name of the sequence will be used as seqname in returned GRanges object.

### Usage

    findORFsFasta(filePath, startCodon = startDefinition(1),
      stopCodon = stopDefinition(1), longestORF = TRUE, minimumLength = 0,
      is.circular = FALSE)

### Arguments

`filePath` | (character) Path to the fasta file.
`startCodon` | (character) Possible START codons to search for. Check [startDefinition()] for helper function.
`stopCodon` | (character) Possible STOP codons to search for. Check [stopDefinition()] for helper function.
`longestORF` | (logical) Default FALSE. When TRUE will only report ORFs that are longest, all smaller overlapping ORFs will be ignored. When FALSE will report all possible ORFs in all three reading frames.
`minimumLength` | (integer) Default is 0. Minimum length of ORF, without counting 3bp for START and STOP codons. For example minimumLength = 8 will result in size of ORFs to be at least START + 8*3 (bp) + STOP. Use this param to restrict search.
`is.circular` | (logical) Whether the genome in filePath is circular. Prokaryotic genomes are usually circular.

### Value

(GRanges) object of ORFs mapped from fasta file. Positions are relative to the fasta file.

### See Also

[findORFs()], [findMapORFs()], [startDefinition()], [stopDefinition()]

Other findORFs: `findMapORFs`, `findORFs`, `startDefinition`, `stopDefinition`

### Examples

    # location of the example fasta file
    example_genome <- system.file("extdata", "genome.fasta", package = "ORFik")
    findORFsFasta(example_genome)

[Package ORFik version 1.0.0 Index]