How else can one quantify a DNA sequence besides GC-content and length?

Question

[jolespin]

I'm looking for other ways of quantifying sequences besides looking at GC-content and length? I could look at coverage and stuff but what about just from the raw sequence? The size of the sequences are gene-length to contig-length of good assemblies (1000 nt - 200 000 nt)

[LauferVA]

the phrasing of your question implies you are looking for quantification related to physical properties.... and probably of a relatively short DNA sequence ... is that correct?

If not, there are TONS of ways. Please disambiguate.

Answer 1

[5heikki]

kmer content

[jolespin]

Can you use this as a single value? I know I could get the % for each kmer in the sequence but I would have multiple values. Maybe stdev of it?

[5heikki]

Well, you could get a single value of e.g. how many unique tetramers there are in a given sequence. I'm not so sure how useful that would be though.

Answer 2

[Pierre Lindenbaum]

Shannon entropy https://books.google.fr/books?id=MRdpjtDbUcQC&lpg=PA56&dq=Shannon%20entropy%20blast&pg=PA55#v=onepage&q=Shannon%20entropy%20blast&f=false

size after compression,

...

Answer 3

[JC]

Time ago I wrote some code for quantify different DNA properties (compositions, bias, complexity): https://github.com/caballero/SeqComplex

Answer 4

[Matt Shirley]

Composition vectors have been used to build phylogenetic trees from sequences: http://www.aporc.org/LNOR/12/ISORA2010F02.pdf

These are somewhat related to kmers though.

Answer 5

[Lars Juhl Jensen]

I hate to bang my own drum, but you can find plenty of DNA structural parameters and other relevant metrics in my work on DNA atlases from 15 years ago (Jensen et al., 1999; Pedersen et al., 2000). This includes parameters such as predicted DNA curvature, flexibility and stability.