Hello,
I am looking for a function that computes a consensus DNA sequence by
plurality. I found "consensus" in bio3d which almost does what I need.
However, it would be important for me to include ambiguities and not to
omit every position that is less than the threshold set in "consensus".
Is anybody aware of a package with a function that includes ambiguities
in a consensus sequence?
Thanks already!
Kim
Here are a couple of sequences to illustrate what I would like:
TGCATACACCGACAACATCCTCGACGACTACACCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
AGCATACACCGACAACATCCTCGATGACTACTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
AGCATACACCGACAACATCCTCGATGACTACTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
CGCCTACACCAACGATGTCCTGGACGACTTCTGCTACTACG
GC TACACC AC A TCCT GA GACT CTGCTACTACG
#This is what I get from "consensus" in bio3d with a threshold of 0.85.
HGCMTACACCRACRAYRTCCTSGAYGACTWCTGCTACTACG
# This is what I would like to get.
___________________________________________
Kim Milferstedt, PhD
Postdoctoral Researcher
University of Illinois at Urbana-Champaign
Department of Microbiology
C207 CLSL
601 S. Goodwin Avenue
Urbana, IL 61801
phone: 001-217-244-0721
email: [EMAIL PROTECTED]
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