Question

Simple subject extraction question with biostrings

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James • 0

@60d686b0

Last seen 2.8 years ago

United States

Hello there! I am new to Biostrings and have what is likely a simple question, but I can't seem to figure out a solution to this issue.

I am doing global pairwise alignments using pairwiseAlignment.

I have an example where the alignment results in three gaps at the start of the sequence. EX:

> align
Global PairwiseAlignmentsSingleSubject (1 of 1)
pattern: ---FLVLLPLVSSQCVNLTTRTQ...GSCCKFDEDDSEPVLKGVKLHYT
subject: MFVFLVLLPLVSSQCVNLTTRTQ...GSCCKFDEDDSEPVLKGVKLHYT
score: 5433.158 
> pattern(align)
[1] FLVLLPLVSSQCVNLTTRTQLPPA...GSCCKFDEDDSEPVLKGVKLHYT 
> subject(align)
[4] FLVLLPLVSSQCVNLTTRTQLPPA...GSCCKFDEDDSEPVLKGVKLHYT

I am in need of having the full sequences including leading gaps (as well as corresponding positions in the subject/reference sequence).

I have discovered how to get the pattern as desired...

> as.character(align)
[1] "---FLVLLPLVSSQCVNLTTRTQ...VLKGVKLHYT

but I can not figure out how one would do this with the subject/ref sequence. I have scoured the documentation, but must be missing something.

If anyone has advice, it would be greatly appreciated!

Biostrings • 987 views

ADD COMMENT • link 2.8 years ago James • 0

score 0 · Answer 1 · 2022-01-27

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DannyM • 0

@dannym-18984

Last seen 11 months ago

Germany

Hi,

can you please provide the code where you generate the alignment?

Best

ADD COMMENT • link 2.8 years ago DannyM • 0

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Thank you for reminding me, I should have added that to the start.

ref <- readAAStringSet('ref.fasta')
study <- readAAStringSet('study.fasta')
align <- pairwiseAlignment(pattern = study[[1]], subject = ref[[1]],type = "global")

ADD REPLY • link 2.8 years ago James • 0