Question: Finding a suitable Independent Variable for a Protein sequence homology analysis
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gravatar for minasmayth
5 weeks ago by
minasmayth0
minasmayth0 wrote:

Hi there everyone!

I am currently working on a paper in which I compare the histone H1 protein sequence of the polar bear and the house mouse, yet one major problem I am having is finding a suitable independent variable, i.e. my experiment is too simplistic. I would like to have something along the lines of the dependent variable being the sequence similarity calculated by a program like BLASTP, and so I was wondering if you all could give me any tips?

Right now I'm thinking along the lines of time since common ancestor divergence (meaning that I would probably add more species for different points of diversion in time), but I'm open for all ideas, options and suggestions!

Thanks in advance! Minas

ADD COMMENTlink modified 23 days ago by Biostar ♦♦ 20 • written 5 weeks ago by minasmayth0

See this Nar article:

H1 histones: current perspectives and challenges

Sean W. Harshman Nicolas L. Young Mark R. Parthun Michael A. Freitas

https://academic.oup.com/nar/article/41/21/9593/1267376

"Eukaryotes also differ in the number of histone H1 variants present. H. sapiens and Mus musculus both have 11 distinct

variants, whereas Caenorhabditis elegans has eight and Xenopus laevis has five (ref.59)."

Who knows, Xenopus laevis looks distant enough to become an outgroup, isn't it?

More mammalian histone H1 would be helpful.

Reference 59 in that article above is not free to me, but probably is useful as well.

"The histone H1 family: specific members, specific functions?"

Annalisa Izzo, Kinga Kamieniarz, Robert Schneider

https://www.degruyter.com/view/j/bchm.2008.389.issue-4/bc.2008.037/bc.2008.037.xml

The following one is a very recent article:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037678/

"Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early

Drosophila embryonic development"

but Drosophila or Yeast are probably too far in your case.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by natasha.sernova3.4k
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