package: Full genome sequences for Brachypodium distachyon (JGI...

In ycl6/BSgenome.Bdistachyon.JGI.Bd3.1: Full genome sequences for Brachypodium distachyon (JGI version 3.0 assembly)

Description

Full genome sequences for Brachypodium distachyon Bd21 (Purple false brome) as provided by the US Department of Energy Joint Genome Institute (DOE-JGI; Phytozome v11) and stored in Biostrings objects. The chloroplast genome is obtained from the NCBI Nucleotide database under the accession EU325680.

Note

This BSgenome data package was made from the following source data files:

Bdistachyon_314_v3.0.fa.gz is obtained from https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Bdistachyon. The chloroplast genome is obtained from http://www.ncbi.nlm.nih.gov/nuccore/EU325680.
  

See ?BSgenomeForge and the BSgenomeForge vignette (vignette("BSgenomeForge")) in the BSgenome software package for how to make a BSgenome data package.

Author(s)

I-Hsuan Lin

See Also

• BSgenome objects and the available.genomes function in the BSgenome software package.

• DNAString objects in the Biostrings package.

• The BSgenomeForge vignette (vignette("BSgenomeForge")) in the BSgenome software package for how to make a BSgenome data package.

Examples

BSgenome.Bdistachyon.JGI.Bd3.1
genome <- BSgenome.Bdistachyon.JGI.Bd3.1
head(seqlengths(genome))
genome$Bd1  # same as genome[["Bd1"]]

## ---------------------------------------------------------------------
## Genome-wide motif searching
## ---------------------------------------------------------------------
## See the GenomeSearching vignette in the BSgenome software
## package for some examples of genome-wide motif searching using
## Biostrings and the BSgenome data packages:
if (interactive())
    vignette("GenomeSearching", package="BSgenome")

ycl6/BSgenome.Bdistachyon.JGI.Bd3.1 documentation built on May 4, 2019, 2:32 p.m.