Question: identify length of repeat arrays with given motif
gravatar for Biomonika (Noolean)
3.7 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:

I am interested in identifying lengths of all stretches of certain repeats (with unit length 5bp-50bp). For example, all occurrences of (GGAAT)n with total length of at least 1000bp. I could write regexp for perfect stretches of the repeats, but since these will likely be imperfect, some Smith-Waterman type of alignment would be better. I will be searching for these repeats per chromosome, so an input will be single large fasta file and a motif to search for.

PS: Software like TRF identifies repeats de novo and I already have list of motifs to search for, I only need to estimate their length distribution

length repeat trf • 790 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 3.7 years ago by Biomonika (Noolean)3.1k
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