What are some of the simplest measures of a "repetitive" nucleotide sequence? simple one seems like entropy, relative to a random nucleotide probability distribution, assuming independence of each base, but this seems incorrect - especially since some repetitive sequences are highly structured and have ORFs.
related question: why is it that LINE1 elements, which have protein coding regions, are classified as repetitive elements? seems incorrect, because their sequence is not repetitive -- it can't be very repetitive if it codes for protein.
thanks for your help.
•
written
by
User 9996
1 answer
Sequences like LINE elements are repetitive because they repeated in the genome, not (directly) because of an intrinsic property of a single LINE element.
Take a look here: http://www.repeatmasker.org/papers.html. As you can see, your question does not have a simple answer.
Log in to answer this question.
-
Proper reanotation of genepanel with snpEff and dbNSFP
written by Lukas •
-
Tutorial: Premade library preparation – considerations, tips and tricks (II)
written by Novogene •
-
Herald: The Biostar Herald for Monday, October 16, 2023
written by Biostar
-
Tutorial: Unsupervised clustering on gene expression data
written by Hamid Ghaedi
-
How to infer unknown gene functions from trajectories of gene expression time series plots?
written by tfhahn •
-
Tutorial: InsideDNA: Analysing raw sequencing reads with FASTQC for quality control and filtering
written by shilparaopradeep •
-
Repetitive motifs on Illumina 450k derived sequences
written by gbayon
-
Issues In Dna Optimization Workflow For Heterologous Expression
written by Ib84 •
-
Statistical Significance Of Sequence-Based Descriptor Data
written by Spyros •
-
Why Doesn'T The "Markov Property" Disqualify Markov Chains For Sequence Analysis?
written by Ib84 •
