{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Demo of script to plot nt imbalance for sequence span\n", "\n", "In order to demonstrate the use of my script `nucleotide_difference_imbalance_plot_stylized_like_Figure_8_of_Morrill_et_al_2016.py`, found [here](https://github.com/fomightez/sequencework/tree/master/plot_nt_imbalance), I'll use it to plot nucleotide difference imbalance for the span of coordinates from the *Saccharomyces cerevisiae* S288C reference sequence that is similar to [Figure 8, panel B](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882425/figure/F8/) of [Morrill et al 2016(PMID: 27026700)](https://www.ncbi.nlm.nih.gov/pubmed/27026700). \n", "This will also demonstrate in the 'Preparation' section use of my script `get_chromosomal_coordinates_as_FASTA.py`, found [here](https://github.com/fomightez/yeastmine), to use YeastMine to retrieve a sequence for a specified region of a *S. cerevisiae* chromosome.\n", "\n", "Full reference for the plot style/approach:\n", "\n", "[DNA Instability Maintains the Repeat Length of the Yeast RNA Polymerase II C-terminal Domain. Morrill SA, Exner AE, Babokhov M, Reinfeld BI, Fuchs SM. J Biol Chem. 2016 May 27;291(22):11540-50. doi: 10.1074/jbc.M115.696252. Epub 2016 Mar 29.(PMID: 27026700)](https://www.ncbi.nlm.nih.gov/pubmed/27026700)\n", "\n", "References for sequence data and YeastMine/Intermine interface used in demonstration: \n", "\n", "[The reference genome sequence of Saccharomyces cerevisiae: then and now. Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM. G3 (Bethesda). 2014 Mar 20;4(3):389-98. doi: 10.1534/g3.113.008995.(PMID: 24374639)](https://www.ncbi.nlm.nih.gov/pubmed/24374639)\n", "\n", "[Saccharomyces Genome Database: the genomics resource of budding yeast. Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED. Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5. doi: 10.1093/nar/gkr1029. Epub 2011 Nov 21. (PMID: 22110037)](https://www.ncbi.nlm.nih.gov/pubmed/22110037)\n", "\n", "[YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, Hong EL, Sullivan J, Micklem G, Cherry JM. Database (Oxford). 2012 Mar 20;2012:bar062. doi: 10.1093/database/bar062. Print 2012.(PMID: 22434830)](https://www.ncbi.nlm.nih.gov/pubmed/22434830)\n", "\n", "[InterMine: extensive web services for modern biology. Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, Hu F, Smith R, Stěpán R, Sullivan J, Micklem G. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W468-72. doi: 10.1093/nar/gku301. Epub 2014 Apr 21.(PMID: 24753429)](https://www.ncbi.nlm.nih.gov/pubmed/24753429)\n", "\n", "\n", "\n", "------" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
If you haven't used one of these notebooks before, they're basically web pages in which you can write, edit, and run live code. They're meant to encourage experimentation, so don't feel nervous. Just try running a few cells and see what happens!.
\n", "\n", "\n", " Some tips:\n", "