| name | bioconductor-bsgenome |
| description | Infrastructure shared by all the Biostrings-based genome data packages. |
| when_to_use | Use when: Chromosome Pattern Matching: Finding or counting the occurrences of an arbitrary nucleotide pattern in a specific chromosome using matchPattern() or countPattern().; Genome-Wide Dictionary Searches: Finding all occurrences of a constant-width dictionary of patterns across an entire genome using PDict() and matchPDict().; Sequence Masking: Applying or toggling masks (e.g., assembly gaps, repeats) o. Not for: For querying remote sequence databases on-the-fly without local storage, use biomaRt instead, as BSgenome relies on locally installed data packages.; For extracting transcript or exon sequences, use GenomicFeatures instead, because BSgenome provides |
| user-invocable | false |
BSgenome
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
- Version: 1.80.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Depends: BiocGenerics, S4Vectors, IRanges, Seqinfo, GenomicRanges, Biostrings, BiocIO, rtracklayer
- Imports: matrixStats, XVector, Rsamtools
- Install:
BiocManager::install("BSgenome")
When to Use
- Chromosome Pattern Matching: Finding or counting the occurrences of an arbitrary nucleotide pattern in a specific chromosome using
matchPattern() or countPattern().
- Genome-Wide Dictionary Searches: Finding all occurrences of a constant-width dictionary of patterns across an entire genome using
PDict() and matchPDict().
- Sequence Masking: Applying or toggling masks (e.g., assembly gaps, repeats) on chromosome sequences using
masks() and active() before performing sequence analysis.
When NOT to Use
- For querying remote sequence databases on-the-fly without local storage, use biomaRt instead, as
BSgenome relies on locally installed data packages.
- For extracting transcript or exon sequences, use GenomicFeatures instead, because
BSgenome provides raw chromosome sequences rather than gene models.
Data Requirements
- Genome Package: An installed
BSgenome data package (e.g., BSgenome.Celegans.UCSC.ce2).
- Query Patterns: A dictionary of patterns stored in a FASTA file and loaded as a
DNAStringSet using readDNAStringSet().
Key Parameters
- max.mismatch (default): Allows inexact matching by specifying the maximum number of mismatching letters per match in
matchPattern().
- fixed (default): Logical or vector controlling whether to allow ambiguities during pattern matching in
countPattern().
- append (default): Logical indicating whether to append results to an existing file in custom output functions.
Best Practices
- Verify Chromosome Information: Use
seqinfo() and seqnames() to verify chromosome naming conventions and lengths before starting an analysis.
- Manage Memory: Load only one chromosome sequence into memory at a time (e.g.,
subject <- genome[[seqname]]) to avoid memory allocation problems on large genomes.
- Reverse Strand Matching: Find matches on the minus strand by taking the
reverseComplement() of the short query pattern rather than the entire chromosome subject.
Common Pitfalls
- Memory Exhaustion: Loading all chromosome sequences into memory at once. Fix: Iterate through chromosomes using a
for loop and seqnames().
- Inefficient Reverse Complementation: Applying
reverseComplement() to an entire chromosome sequence. Fix: Apply reverseComplement() to the short query pattern instead.
- Masking Confusion: Forgetting that masks might be active, leading to skipped matches or unexpected results. Fix: Explicitly toggle masks using
active(masks(chrY)) <- FALSE.
Alternatives
- Biostrings: For basic sequence manipulation on individual FASTA files without the full genome package infrastructure.
- GenomicFeatures: For extracting transcript/exon sequences rather than raw genomic intervals.
- biomaRt: For querying remote sequence databases without local storage.
Citations
- Pagès, H. (2026). Efficient genome searching with Biostrings and the BSgenome data packages.
References
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