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Codon Bias

Add MS 86696 : 1987-1995

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  • Title:
    Codon Bias
  • Collection Area: Western Manuscripts
  • Reference: Add MS 86696
  • Creation Date: 1987-1995
  • Extent and Access:
    Extent: 5 sub-folders

  • Language: English
  • Contents and Scope:
    Contents:

    Some items are undated.

    Folder marked 'Codon bias in Neisseria'.

    • Computer printout for 'cai'; 27 Jan 1994.
    • Computer listing for "cai"; 27 Jan 1994.
    • Computer printout for "coduse"; 16 Jan 1995.
    • Computer printout for '"coduse" on reca'; 16 Jan 1995.
    • Computer printout for 'coduse' on neiss.shik; 16 Jan 1995.
    • Computer printout for a run of 'coduse' on neiss.por; 17 Jan 1995.
    • Handwritten notes on "coduse" and "cai"; Apr 1995.
    • Handwritten figures relating to neisseria – 3rd site divergence; Jun 1995.
    • Handwritten list of programs; 20 Dec 1995. Includes notes about each program.
    • Handwritten notes relating to codon adaptation index. Attached to Paul M. Sharp and Wen-Hsiung Li, 'The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications', Nucleid Acids Research , 15 (1987), 1281-6.
    • Handwritten figures for 'codon usage in E.coli'.
    • Article by unknown author 'Cloned N. Gonorrhoea genes and codon usage', Clinical Microbiological Review , 2 (1989), S93-S95.

    Folder marked 'Bias programs "bias" "bione"'.

    • Computer printout for 'bias' run 2; 1 Aug 1994.
    • Computer printout for 'bias' run 11; 4 Aug 1994.
    • Computer printout for 'bione' run 1A; 5 Aug 1994.
    • Computer printout for 'bias1' run 1; 14 Aug 1994.
    • Computer printout for 'bias1'; 15 Aug 1994.
    • Handwritten notes relating to 'program "bias1" and "bias2".
    • Computer printout for '"bias2" and runs'.
    • Handwritten table of data.
    • Handwritten notes relating to 'checking "bione" against Bulmer's theory'.
    • Computer printout for 'bione' run 3.
    • Computer printout for 'bione' run 1.
    • Computer printout for 'bione' run 2.
    • Handwritten notes on 'bias' run 14.
    • Computer printout for 'bias' run 15.

    Folder marked 'Codon bias in Hlc gene, TAR gene, program "hlcbias" and codon bias in Ecoli/salmonella genes at changed and unchanged sites Program "bias"'

    • Computer printouts of DNA sequences; 26 Aug 1992.
    • Computer printout for '"colbias" listing and runs'.
    • Handwritten notes relating to 'codon bias at synonymous and substituted codons'.
    • Computer printout for 'cslbias'.
    • Workings out and photocopied hand drawn graph.
    • Computer printouts for 'bias'.
    • Computer printout for 'bias' on genes differing by decrease 20% nucleotides.
    • Computer printout for "bias" on genes with nt% difference under 10%
    • Handwritten data tables on 'difference %'
    • Computer printout of 'bias' on genes with 10-15% difference.
    • Computer printout for runs of 'hlcbias' on gene TAR.

    Folder marked 'Codon bias in infinite P & Pn. Brought forth a mouse!'

    • Computer printout for 'popbias1'; 5 Oct 1995.
    • Computer printout for 'popbias 2'; 6 Oc 1995.
    • Handwritten notes on 'where we stand on codon bias'.
    • Handwritten notes relating to mutations in codon bias.

    Folder marked 'Reverse bias or bias if varying degree?'

    • Handwritten notes on reverse bias, two copies, one photocopy; 23 Oct 1995.

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