Dear listserv,
I don't know if this question is more appropriate for the Bioconductor listserv
or the general R listserv. I am asking it here because I believe this problem
can be solved using regular R commands in the base package. I suspect you all
will be very helpful.
I have genetic sequence data in the following form. Each letter represents a
nucleotide.
ref.sequence <- "ATAGCCGCA"
sequence1 <- "AT[G][C][C]AGCCG[T]CA"
sequence2 <- "ATAGCCGC[C][A][C]A"
sequence3 <- "AT[GCC]AGCCGCA"
The brackets indicate nucleotide "insertions" relative to the reference
sequence ("ref.sequence"). Some sequences may have some/all of the insertions,
some may not.
What I want is for all of the positions to "align" (line up) properly.
Therefore, the sequences lacking a particular insertion should get scored with
a dash (or dashes) at that position.
I want to end up with this:
ref.sequence should look like this: "AT---AGCCG-C---A"
sequence1 should look like this: "AT[G][C][C]AGCCG[T]C---A"
sequence2 should look like this: "AT---AGCCG-C[C][A][C]A"
sequence3 should look like this: "AT[G][C][C]AGCCG-C---A"
So how can I make this happen efficiently?
Thanks very much in advance,
-----------------------------------
Josh Banta, Ph.D
Assistant Professor
Department of Biology
The University of Texas at Tyler
Tyler, TX 75799
Tel: (903) 565-5655
http://plantevolutionaryecology.org
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