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Full masked genome sequences for Canis lupus familiaris (UCSC version canFam3)

Bioconductor version: Release (3.19)

Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

Author: The Bioconductor Dev Team

Maintainer: Bioconductor Package Maintainer <maintainer at>

Citation (from within R, enter citation("BSgenome.Cfamiliaris.UCSC.canFam3.masked")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews AnnotationData, BSgenome, Canis_familiaris, Genetics
Version 1.3.99
License Artistic-2.0
Depends BSgenome(>= 1.31.8), BSgenome.Cfamiliaris.UCSC.canFam3
Imports BSgenome, BSgenome.Cfamiliaris.UCSC.canFam3
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Source Package BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz
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