Introduction to Biostrings

Introduction to Bioconductor in R

James Chapman

Curriculum Manager, DataCamp

Biostrings

Algorithms for fast manipulation of sequences
Many Bioconductor packages are dependent on Biostrings

BiocManager::install("Biostrings")

Biological string containers

Biostrings → Memory efficient to store and manipulate sequence of characters
Containers that can be inherited

For example:

The BString class comes from big string

Strings vs. Sets

XString to store a single sequence
- BString for any string
- DNAString for DNA
- RNAString for RNA
- AAString for amino acids

XStringSet for many sequences
- BStringSet
- DNAStringSet
- RNAStringSet
- AAStringSet

showClass()

showClass("XString")

Virtual Class "XString" [package "Biostrings"]

Slots:

Name:             shared            offset            length   elementMetadata          metadata
Class:         SharedRaw           integer           integer DataFrame_OR_NULL              list

Extends: 
Class "XRaw", directly
Class "XVector", by class "XRaw", distance 2
Class "Vector", by class "XRaw", distance 3
Class "Annotated", by class "XRaw", distance 4
Class "vector_OR_Vector", by class "XRaw", distance 4

Known Subclasses: "BString", "DNAString", "RNAString", "AAString"

Biostring alphabets

DNA_BASES # 4 DNA bases

RNA_BASES # 4 RNA bases

"A" "C" "G" "T"

"A" "C" "G" "U"

AA_STANDARD # 20 Amino acids

"A" "R" "N" "D" "C" "Q" "E" "G" "H" "I" "L" "K" "M" "F" "P" "S" "T" "W" "Y" "V"

DNA_ALPHABET # contains IUPAC_CODE_MAP 
RNA_ALPHABET # contains IUPAC_CODE_MAP 
AA_ALPHABET  # contains AMINO_ACID_CODE

¹ For more information IUPAC DNA codes http://genome.ucsc.edu/goldenPath/help/iupac.html

transcription and translation

Transcription DNA to RNA

# DNA single string
dna_seq <- DNAString("ATGATCTCGTAA")
dna_seq

12-letter DNAString object
seq: ATGATCTCGTAA

# Transcription DNA to RNA string
rna_seq <- RNAString(dna_seq)
rna_seq

12-letter RNAString object
seq: AUGAUCUCGUAA

Translation RNA to amino acids

rna_seq

12-letter RNAString object 
seq: AUGAUCUCGUAA

# Translation RNA to AA
aa_seq <- translate(rna_seq)
aa_seq

Three RNA bases form one AA: AUG = M, AUC = I, UCG = S, UAA = *

4-letter AAString object
seq: MIS*

Shortcut translate DNA to amino acids

dna_seq

12-letter DNAString object
seq: ATGATCTCGTAA

# translate() also goes directly from DNA to AA
translate(dna_seq)

4-letter AAString object
seq: MIS*

The Zika virus

Zika virus

Zika symptoms

Let's practice with the Zika virus!

Introduction to Bioconductor in R