Generate a sequence of specific length with a list of motifs and intersperse with spacers

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2.9 years ago

rykerklie7 ▴ 30

I have a list of motifs and would like to create sequences with all possible combinations and length 127-131nt. Two motifs in the sequence should also be interspersed with spacers (random letters composed of ACGT in any order). The spacers can be of length 5nt or 10nt. So the sequence will be something like below but of length between 127nt-131nt including the motifs and spacers.

       MOTIF1(length 7nt)SPACER(5nt)MOTIF2(length8nt)SPACER(10nt)MOTIF3(length5nt)...

Is there any program or package in R that does this?

python R perl motif sequence • 837 views

ADD COMMENT • link updated 4 months ago by mopejij688 • 0 • written 2.9 years ago by rykerklie7 ▴ 30

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use recursion.

see Degenerate Nucleotide Sequences or creating virtual library preparation of all possible exons in a gene in human for an example.

ADD REPLY • link 2.9 years ago by Pierre Lindenbaum 161k

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This server almost does what you need. I don't think spacer length can be defined.

ADD REPLY • link 2.9 years ago by Mensur Dlakic ★ 27k

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