mercator: Run mercator to build a homology map and create orthologous...

In gschofl/genoslideR: Create and manipulate multiple genome alignments with annotation.

Description

Run mercator to build a homology map and create orthologous segments that can be aligned using FSA

Usage

mercator(seq_files, anno_files = NULL, anno_type = "glimmer3",
  glimmeropts = list(o = 50, g = 110, t = 30), removeOverlappingCDS = TRUE,
  mask = TRUE, wd = NULL)

Arguments

seq_files	Path to sequence files ('fasta' or 'genbank').
anno_files	(Optional) Path to annotation files. If no annotation files are provided an ab initio annotation using glimmer3 is performed.
anno_type	Type of annotation ('glimmer3', 'genbank', 'gff', 'ptt', or 'ftable').
glimmeropts	Options passed to glimmer3 if an ab initio annotation is performed.
removeOverlappingCDS	Exclude overlapping CDS for orthology mapping.
mask	Softmask sequence before aligning using maskSequence.
wd	Working directory. Defaults to the parent directory of the provided sequence files.

Details

mercator will create a hidden directory ‘.mercator’ in the parent directory of the submitted sequence files and place all results of the intermediate computational steps in this directory.

The results of a mercator run are stored in a directory ‘segments’ in the parent directory of the submitted sequence files. The ‘segments’ directory should contain numbered subdirectories containing orthologous genomic segments in multi fasta format, a file named ‘map’, and a file named ‘genomes’.

mercator segements can be aligned using the alignSegments function, merged into a single multi-fasta alignment file and imported into R as a DNAStringSet using importAlignment or imported to R as an annotatedAlignment using annotatedAlignment.

See Also

alignSegments, importAlignment, annotatedAlignment.

gschofl/genoslideR documentation built on May 17, 2019, 8:52 a.m.