Sequence handling

Introduction to Bioconductor in R

James Chapman

Curriculum Manager, DataCamp

Single vs. Set

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

Create a StringSet and collate it

# Read the sequence as a set
zikaVirus <- readDNAStringSet("data/zika.fa")

length(zikaVirus)  # the set contains only one sequence
width(zikaVirus)   # and width 10794 bases

1
10794

# Collate the sequence
zikaVirus_seq <- unlist(zikaVirus)


length(zikaVirus_seq)

width(zikaVirus_seq)

10794

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘width’ for signature ‘"DNAString"’

From a single sequence to a set

# to create a new set from a single sequence
zikaSet <- DNAStringSet(zikaVirus_seq, start = c(1, 101, 201), end = c(100, 200, 300))
zikaSet

DNAStringSet object of length 3:
    width seq
[1]   100 AGTTGTTGATCTGTGTGAGTCAGACTGCGACAGTTCGAGTCTGAAG...AACAACAGTATCAACAGGTTTAATTTGGATTTGGAAACGAGAGTTT
[2]   100 CTGGTCATGAAAAACCCCAAAGAAGAAATCCGGAGGATCCGGATTG...CTAAAACGCGGAGTAGCCCGTGTAAACCCCTTGGGAGGTTTGAAGA
[3]   100 GGTTGCCAGCCGGACTTCTGCTGGGTCATGGACCCATCAGAATGGT...TACTAGCCTTTTTGAGATTTACAGCAATCAAGCCATCACTGGGCCT

length(zikaSet) 
width(zikaSet)

3
100 100 100

Complement sequence

ATGATCTCGTAA

a_seq <- DNAString("ATGATCTCGTAA")
a_seq

12-letter DNAString object
seq: ATGATCTCGTAA

complement(a_seq)

12-letter DNAString object
seq: TACTAGAGCATT

Rev a sequence

zikaShortSet

DNAStringSet instance of length 2
width seq                          names      
[1]    18 AGTTGTTGATCTGTGTGA        seq1
[2]    18 CTGGTCATGAAAAACCCC        seq2

rev(zikaShortSet)

 A DNAStringSet instance of length 2
width seq                          names      
[1]    18 CTGGTCATGAAAAACCCC        seq2       
[2]    18 AGTTGTTGATCTGTGTGA        seq1

Reverse a sequence

zikaShortSet

 A DNAStringSet instance of length 2
width seq                          names      
[1]    18 AGTTGTTGATCTGTGTGA        seq1
[2]    18 CTGGTCATGAAAAACCCC        seq2

reverse(zikaShortSet)

 A DNAStringSet instance of length 2
width seq                          names    
[1]    18 AGTGTGTCTAGTTGTTGA        seq1
[2]    18 CCCCAAAAAGTACTGGTC        seq2

Reverse complement

# Original rna_seq sequence
8-letter RNAString object
seq: AGUUGUUG

reverseComplement(rna_seq)

8-letter RNAString object
seq: CAACAACU

# Using two functions together
reverse(complement(rna_seq))

8-letter RNAString object
seq: CAACAACU

unlist length width complement rev reverse everseComplement

Let's practice sequence handling!

Introduction to Bioconductor in R