Following the Biostrings vignettes and the DECIPHER vignette: “The Art of Multiple Sequence Alignment in R”.
At least once, you must install DECIPHER (and Biostrings).
source("http://bioconductor.org/biocLite.R")
biocLite("DECIPHER")Load Biostrings, read in example data, and display the unaligned sequences.
library(Biostrings)## Loading required package: BiocGenerics## Loading required package: parallel##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB## The following objects are masked from 'package:stats':
##
## IQR, mad, xtabs## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, as.vector, cbind,
## colnames, do.call, duplicated, eval, evalq, Filter, Find, get,
## grep, grepl, intersect, is.unsorted, lapply, lengths, Map,
## mapply, match, mget, order, paste, pmax, pmax.int, pmin,
## pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
## setdiff, sort, table, tapply, union, unique, unlist, unsplit## Loading required package: S4Vectors## Loading required package: stats4## Loading required package: IRanges## Loading required package: XVectora1 <- pairwiseAlignment(pattern="acacacta", subject="agcacacac", gapOpening=1, gapExtension=0)
a1## Global PairwiseAlignmentsSingleSubject (1 of 1)
## pattern: [1] a-cacacta
## subject: [1] agcacac-a
## score: 10.87229We can specify a substitution matrix with the scores we want.
mat <- nucleotideSubstitutionMatrix(match = 0, mismatch = -1, baseOnly = TRUE)
a1 <- pairwiseAlignment(DNAString("acacactac"),
DNAString("agcacacac"),
gapOpening=1,
gapExtension=0,
substitutionMatrix=mat)
a1## Global PairwiseAlignmentsSingleSubject (1 of 1)
## pattern: [1] A-CACACTAC
## subject: [1] AGCACAC-AC
## score: -2Download protein sequences for two isoforms of BRCA1:
We can use Biostrings::readAAStringSet to read in the fasta format files.
s1 <- readAAStringSet("NP_009231.2.fa")
s2 <- readAAStringSet("NP_009225.1.fa")These sequences can be aligned with amino acid substituition matrices:
pw <- pairwiseAlignment(s1, s2)The resulting alignment can be written out to a text file.
writePairwiseAlignments(pw, file="test.pair")We will use the DECIPHER library for additional analyses.
library(DECIPHER)## Loading required package: RSQLite## Loading required package: DBIWe can also read in a set of fasta formatted sequences all at the same time.
fas <- system.file("extdata", "50S_ribosomal_protein_L2.fas", package="DECIPHER")
dna <- readDNAStringSet(fas)
dna## A DNAStringSet instance of length 317
## width seq names
## [1] 819 ATGGCTTTAAAAAATTTTAA...TATTGTAAAAAAAAGAAAA Rickettsia prowaz...
## [2] 822 ATGGGAATACGTAAACTCAA...CATTGAGAGAAGGAAAAAG Porphyromonas gin...
## [3] 822 ATGGGAATACGTAAACTCAA...CATTGAGAGAAGGAAAAAG Porphyromonas gin...
## [4] 822 ATGGGAATACGTAAACTCAA...CATTGAGAGAAGGAAAAAG Porphyromonas gin...
## [5] 819 ATGGCTATCGTTAAATGTAA...CGTACGTCGTCGTGGTAAA Pasteurella multo...
## ... ... ...
## [313] 819 ATGGCAATTGTTAAATGTAA...CGTACGTCGCCGTACTAAA Pectobacterium at...
## [314] 822 ATGCCTATTCAAAAATGCAA...TCGCGATCGTCGCGTCAAG Acinetobacter sp....
## [315] 864 ATGGGCATTCGCGTTTACCG...TCGCGGTGGTCGTCAGTCT Thermosynechococc...
## [316] 831 ATGGCACTGAAGACATTCAA...CCGCCACAAGCGGAAGAAG Bradyrhizobium ja...
## [317] 840 ATGGGCATTCGCAAATATCG...GACGGCTTCCGGGCGAGGT Gloeobacter viola...The dna object has 317 sequences of around 900 bases from different organism’s 50S ribosomal subunit.
Translate the DNA to amino acids and align the peptides, then browse the resulting alignment.
AA <- AlignTranslation(dna, asAAStringSet=TRUE)## Determining distance matrix based on shared 4-mers:
##
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 9%
|
|====== | 10%
|
|======= | 11%
|
|======== | 12%
|
|======== | 13%
|
|========= | 14%
|
|========== | 15%
|
|========== | 16%
|
|=========== | 17%
|
|============ | 18%
|
|============ | 19%
|
|============= | 20%
|
|============== | 21%
|
|============== | 22%
|
|=============== | 23%
|
|================ | 24%
|
|================ | 25%
|
|================= | 26%
|
|================== | 27%
|
|================== | 28%
|
|=================== | 29%
|
|==================== | 30%
|
|==================== | 31%
|
|===================== | 32%
|
|===================== | 33%
|
|====================== | 34%
|
|======================= | 35%
|
|======================= | 36%
|
|======================== | 37%
|
|========================= | 38%
|
|========================= | 39%
|
|========================== | 40%
|
|=========================== | 41%
|
|=========================== | 42%
|
|============================ | 43%
|
|============================= | 44%
|
|============================= | 45%
|
|============================== | 46%
|
|=============================== | 47%
|
|=============================== | 48%
|
|================================ | 49%
|
|================================ | 50%
|
|================================= | 51%
|
|================================== | 52%
|
|================================== | 53%
|
|=================================== | 54%
|
|==================================== | 55%
|
|==================================== | 56%
|
|===================================== | 57%
|
|====================================== | 58%
|
|====================================== | 59%
|
|======================================= | 60%
|
|======================================== | 61%
|
|======================================== | 62%
|
|========================================= | 63%
|
|========================================== | 64%
|
|========================================== | 65%
|
|=========================================== | 66%
|
|============================================ | 67%
|
|============================================ | 68%
|
|============================================= | 69%
|
|============================================== | 70%
|
|============================================== | 71%
|
|=============================================== | 72%
|
|=============================================== | 73%
|
|================================================ | 74%
|
|================================================= | 75%
|
|================================================= | 76%
|
|================================================== | 77%
|
|=================================================== | 78%
|
|=================================================== | 79%
|
|==================================================== | 80%
|
|===================================================== | 81%
|
|===================================================== | 82%
|
|====================================================== | 83%
|
|======================================================= | 84%
|
|======================================================= | 85%
|
|======================================================== | 86%
|
|========================================================= | 87%
|
|========================================================= | 88%
|
|========================================================== | 89%
|
|========================================================== | 90%
|
|=========================================================== | 91%
|
|============================================================ | 92%
|
|============================================================ | 93%
|
|============================================================= | 94%
|
|============================================================== | 95%
|
|============================================================== | 96%
|
|=============================================================== | 97%
|
|================================================================ | 98%
|
|================================================================ | 99%
|
|=================================================================| 100%
##
## Time difference of 0.16 secs
##
## Clustering into groups by similarity:
##
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 9%
|
|====== | 10%
|
|======= | 11%
|
|======== | 12%
|
|======== | 13%
|
|========= | 14%
|
|========== | 15%
|
|========== | 16%
|
|=========== | 17%
|
|============ | 18%
|
|============ | 19%
|
|============= | 20%
|
|============== | 21%
|
|============== | 22%
|
|=============== | 23%
|
|================ | 24%
|
|================ | 25%
|
|================= | 26%
|
|================== | 27%
|
|================== | 28%
|
|=================== | 29%
|
|==================== | 30%
|
|==================== | 31%
|
|===================== | 32%
|
|===================== | 33%
|
|====================== | 34%
|
|======================= | 35%
|
|======================= | 36%
|
|======================== | 37%
|
|========================= | 38%
|
|========================= | 39%
|
|========================== | 40%
|
|=========================== | 41%
|
|=========================== | 42%
|
|============================ | 43%
|
|============================= | 44%
|
|============================= | 45%
|
|============================== | 46%
|
|=============================== | 47%
|
|=============================== | 48%
|
|================================ | 49%
|
|================================ | 50%
|
|================================= | 51%
|
|================================== | 52%
|
|================================== | 53%
|
|=================================== | 54%
|
|==================================== | 55%
|
|==================================== | 56%
|
|===================================== | 57%
|
|====================================== | 58%
|
|====================================== | 59%
|
|======================================= | 60%
|
|======================================== | 61%
|
|======================================== | 62%
|
|========================================= | 63%
|
|========================================== | 64%
|
|========================================== | 65%
|
|=========================================== | 66%
|
|============================================ | 67%
|
|============================================ | 68%
|
|============================================= | 69%
|
|============================================== | 70%
|
|============================================== | 71%
|
|=============================================== | 72%
|
|=============================================== | 73%
|
|================================================ | 74%
|
|================================================= | 75%
|
|================================================= | 76%
|
|================================================== | 77%
|
|=================================================== | 78%
|
|=================================================== | 79%
|
|==================================================== | 80%
|
|===================================================== | 81%
|
|===================================================== | 82%
|
|====================================================== | 83%
|
|======================================================= | 84%
|
|======================================================= | 85%
|
|======================================================== | 86%
|
|========================================================= | 87%
|
|========================================================= | 88%
|
|========================================================== | 89%
|
|========================================================== | 90%
|
|=========================================================== | 91%
|
|============================================================ | 92%
|
|============================================================ | 93%
|
|============================================================= | 94%
|
|============================================================== | 95%
|
|============================================================== | 96%
|
|=============================================================== | 97%
|
|================================================================ | 98%
|
|================================================================ | 99%
|
|=================================================================| 100%
##
## Time difference of 0.55 secs
##
## Aligning Sequences:
##
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 9%
|
|====== | 10%
|
|======= | 11%
|
|======== | 12%
|
|======== | 13%
|
|========= | 14%
|
|========== | 15%
|
|========== | 16%
|
|=========== | 17%
|
|============ | 18%
|
|============ | 19%
|
|============= | 20%
|
|============== | 21%
|
|============== | 22%
|
|=============== | 23%
|
|================ | 24%
|
|================ | 25%
|
|================= | 26%
|
|================== | 27%
|
|================== | 28%
|
|=================== | 29%
|
|==================== | 30%
|
|==================== | 31%
|
|===================== | 32%
|
|===================== | 33%
|
|====================== | 34%
|
|======================= | 35%
|
|======================= | 36%
|
|======================== | 37%
|
|========================= | 38%
|
|========================= | 39%
|
|========================== | 40%
|
|=========================== | 41%
|
|=========================== | 42%
|
|============================ | 43%
|
|============================= | 44%
|
|============================= | 45%
|
|============================== | 46%
|
|=============================== | 47%
|
|=============================== | 48%
|
|================================ | 49%
|
|================================ | 50%
|
|================================= | 51%
|
|================================== | 52%
|
|================================== | 53%
|
|=================================== | 54%
|
|==================================== | 55%
|
|==================================== | 56%
|
|===================================== | 57%
|
|====================================== | 58%
|
|====================================== | 59%
|
|======================================= | 60%
|
|======================================== | 61%
|
|======================================== | 62%
|
|========================================= | 63%
|
|========================================== | 64%
|
|========================================== | 65%
|
|=========================================== | 66%
|
|============================================ | 67%
|
|============================================ | 68%
|
|============================================= | 69%
|
|============================================== | 70%
|
|============================================== | 71%
|
|=============================================== | 72%
|
|=============================================== | 73%
|
|================================================ | 74%
|
|================================================= | 75%
|
|================================================= | 76%
|
|================================================== | 77%
|
|=================================================== | 78%
|
|=================================================== | 79%
|
|==================================================== | 80%
|
|===================================================== | 81%
|
|===================================================== | 82%
|
|====================================================== | 83%
|
|======================================================= | 84%
|
|======================================================= | 85%
|
|======================================================== | 86%
|
|========================================================= | 87%
|
|========================================================= | 88%
|
|========================================================== | 89%
|
|========================================================== | 90%
|
|=========================================================== | 91%
|
|============================================================ | 92%
|
|============================================================ | 93%
|
|============================================================= | 94%
|
|============================================================== | 95%
|
|============================================================== | 96%
|
|=============================================================== | 97%
|
|================================================================ | 98%
|
|================================================================ | 99%
|
|=================================================================| 100%
##
## Time difference of 8.64 secs
##
## Determining distance matrix based on alignment:
##
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 9%
|
|====== | 10%
|
|======= | 11%
|
|======== | 12%
|
|======== | 13%
|
|========= | 14%
|
|========== | 15%
|
|========== | 16%
|
|=========== | 17%
|
|============ | 18%
|
|============ | 19%
|
|============= | 20%
|
|============== | 21%
|
|============== | 22%
|
|=============== | 23%
|
|================ | 24%
|
|================ | 25%
|
|================= | 26%
|
|================== | 27%
|
|================== | 28%
|
|=================== | 29%
|
|==================== | 30%
|
|==================== | 31%
|
|===================== | 32%
|
|===================== | 33%
|
|====================== | 34%
|
|======================= | 35%
|
|======================= | 36%
|
|======================== | 37%
|
|========================= | 38%
|
|========================= | 39%
|
|========================== | 40%
|
|=========================== | 41%
|
|=========================== | 42%
|
|============================ | 43%
|
|============================= | 44%
|
|============================= | 45%
|
|============================== | 46%
|
|=============================== | 47%
|
|=============================== | 48%
|
|================================ | 49%
|
|================================ | 50%
|
|================================= | 51%
|
|================================== | 52%
|
|================================== | 53%
|
|=================================== | 54%
|
|==================================== | 55%
|
|==================================== | 56%
|
|===================================== | 57%
|
|====================================== | 58%
|
|====================================== | 59%
|
|======================================= | 60%
|
|======================================== | 61%
|
|======================================== | 62%
|
|========================================= | 63%
|
|========================================== | 64%
|
|========================================== | 65%
|
|=========================================== | 66%
|
|============================================ | 67%
|
|============================================ | 68%
|
|============================================= | 69%
|
|============================================== | 70%
|
|============================================== | 71%
|
|=============================================== | 72%
|
|=============================================== | 73%
|
|================================================ | 74%
|
|================================================= | 75%
|
|================================================= | 76%
|
|================================================== | 77%
|
|=================================================== | 78%
|
|=================================================== | 79%
|
|==================================================== | 80%
|
|===================================================== | 81%
|
|===================================================== | 82%
|
|====================================================== | 83%
|
|======================================================= | 84%
|
|======================================================= | 85%
|
|======================================================== | 86%
|
|========================================================= | 87%
|
|========================================================= | 88%
|
|========================================================== | 89%
|
|========================================================== | 90%
|
|=========================================================== | 91%
|
|============================================================ | 92%
|
|============================================================ | 93%
|
|============================================================= | 94%
|
|============================================================== | 95%
|
|============================================================== | 96%
|
|=============================================================== | 97%
|
|================================================================ | 98%
|
|================================================================ | 99%
|
|=================================================================| 100%
##
## Time difference of 0.03 secs
##
## Reclustering into groups by similarity:
##
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 9%
|
|====== | 10%
|
|======= | 11%
|
|======== | 12%
|
|======== | 13%
|
|========= | 14%
|
|========== | 15%
|
|========== | 16%
|
|=========== | 17%
|
|============ | 18%
|
|============ | 19%
|
|============= | 20%
|
|============== | 21%
|
|============== | 22%
|
|=============== | 23%
|
|================ | 24%
|
|================ | 25%
|
|================= | 26%
|
|================== | 27%
|
|================== | 28%
|
|=================== | 29%
|
|==================== | 30%
|
|==================== | 31%
|
|===================== | 32%
|
|===================== | 33%
|
|====================== | 34%
|
|======================= | 35%
|
|======================= | 36%
|
|======================== | 37%
|
|========================= | 38%
|
|========================= | 39%
|
|========================== | 40%
|
|=========================== | 41%
|
|=========================== | 42%
|
|============================ | 43%
|
|============================= | 44%
|
|============================= | 45%
|
|============================== | 46%
|
|=============================== | 47%
|
|=============================== | 48%
|
|================================ | 49%
|
|================================ | 50%
|
|================================= | 51%
|
|================================== | 52%
|
|================================== | 53%
|
|=================================== | 54%
|
|==================================== | 55%
|
|==================================== | 56%
|
|===================================== | 57%
|
|====================================== | 58%
|
|====================================== | 59%
|
|======================================= | 60%
|
|======================================== | 61%
|
|======================================== | 62%
|
|========================================= | 63%
|
|========================================== | 64%
|
|========================================== | 65%
|
|=========================================== | 66%
|
|============================================ | 67%
|
|============================================ | 68%
|
|============================================= | 69%
|
|============================================== | 70%
|
|============================================== | 71%
|
|=============================================== | 72%
|
|=============================================== | 73%
|
|================================================ | 74%
|
|================================================= | 75%
|
|================================================= | 76%
|
|================================================== | 77%
|
|=================================================== | 78%
|
|=================================================== | 79%
|
|==================================================== | 80%
|
|===================================================== | 81%
|
|===================================================== | 82%
|
|====================================================== | 83%
|
|======================================================= | 84%
|
|======================================================= | 85%
|
|======================================================== | 86%
|
|========================================================= | 87%
|
|========================================================= | 88%
|
|========================================================== | 89%
|
|========================================================== | 90%
|
|=========================================================== | 91%
|
|============================================================ | 92%
|
|============================================================ | 93%
|
|============================================================= | 94%
|
|============================================================== | 95%
|
|============================================================== | 96%
|
|=============================================================== | 97%
|
|================================================================ | 98%
|
|================================================================ | 99%
|
|=================================================================| 100%
##
## Time difference of 0.55 secs
##
## Realigning Sequences:
##
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 9%
|
|====== | 10%
|
|======= | 11%
|
|======== | 12%
|
|======== | 13%
|
|========= | 14%
|
|========== | 15%
|
|========== | 16%
|
|=========== | 17%
|
|============ | 18%
|
|============ | 19%
|
|============= | 20%
|
|============== | 21%
|
|============== | 22%
|
|=============== | 23%
|
|================ | 24%
|
|================ | 25%
|
|================= | 26%
|
|================== | 27%
|
|================== | 28%
|
|=================== | 29%
|
|==================== | 30%
|
|==================== | 31%
|
|===================== | 32%
|
|===================== | 33%
|
|====================== | 34%
|
|======================= | 35%
|
|======================= | 36%
|
|======================== | 37%
|
|========================= | 38%
|
|========================= | 39%
|
|========================== | 40%
|
|=========================== | 41%
|
|=========================== | 42%
|
|============================ | 43%
|
|============================= | 44%
|
|============================= | 45%
|
|============================== | 46%
|
|=============================== | 47%
|
|=============================== | 48%
|
|================================ | 49%
|
|================================ | 50%
|
|================================= | 51%
|
|================================== | 52%
|
|================================== | 53%
|
|=================================== | 54%
|
|==================================== | 55%
|
|==================================== | 56%
|
|===================================== | 57%
|
|====================================== | 58%
|
|====================================== | 59%
|
|======================================= | 60%
|
|======================================== | 61%
|
|======================================== | 62%
|
|========================================= | 63%
|
|========================================== | 64%
|
|========================================== | 65%
|
|=========================================== | 66%
|
|============================================ | 67%
|
|============================================ | 68%
|
|============================================= | 69%
|
|============================================== | 70%
|
|============================================== | 71%
|
|=============================================== | 72%
|
|=============================================== | 73%
|
|================================================ | 74%
|
|================================================= | 75%
|
|================================================= | 76%
|
|================================================== | 77%
|
|=================================================== | 78%
|
|=================================================== | 79%
|
|==================================================== | 80%
|
|===================================================== | 81%
|
|===================================================== | 82%
|
|====================================================== | 83%
|
|======================================================= | 84%
|
|======================================================= | 85%
|
|======================================================== | 86%
|
|========================================================= | 87%
|
|========================================================= | 88%
|
|========================================================== | 89%
|
|========================================================== | 90%
|
|=========================================================== | 91%
|
|============================================================ | 92%
|
|============================================================ | 93%
|
|============================================================= | 94%
|
|============================================================== | 95%
|
|============================================================== | 96%
|
|=============================================================== | 97%
|
|================================================================ | 98%
|
|================================================================ | 99%
|
|=================================================================| 100%
##
## Time difference of 9.82 secs
##
## Refining the alignment:
##
|
| | 0%
|
|=================================================================| 100%
##
## Time difference of 0 secsBrowseSeqs(AA, htmlFile="ribo.html", openURL = FALSE, highlight=1)You should now have a file called ribo.html with the aligned sequences. You can open the alignment in RStudio and send it to your web browser.