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)
5 answers
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,
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written
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Pierre Lindenbaum
Time ago I wrote some code for quantify different DNA properties (compositions, bias, complexity): https://github.com/caballero/SeqComplex
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.
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written
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Matt Shirley
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.
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Lars Juhl Jensen
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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.