CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1LSE_1 1VYS_1 2DNA_1 Letter Amino acid
12 46 7 A Alanine
14 15 4 N Asparagine
7 18 2 D Aspartic acid
8 1 1 C Cysteine
7 17 2 T Threonine
11 25 1 R Arginine
12 34 8 G Glycine
6 23 2 I Isoleucine
2 3 2 M Methionine
10 23 12 S Serine
3 14 2 Y Tyrosine
1 9 1 H Histidine
3 10 3 F Phenylalanine
6 21 2 V Valine
3 15 4 Q Glutamine
2 26 3 E Glutamic acid
8 30 5 L Leucine
6 12 3 K Lycine
2 20 3 P Proline
6 2 0 W Tryptophan 

1LSE_1|Chain A|HEN EGG WHITE LYSOZYME|Gallus gallus (9031)
>1VYS_1|Chain A[auth X]|PENTAERYTHRITOL TETRANITRATE REDUCTASE|ENTEROBACTER CLOACAE (550)
>2DNA_1|Chain A|unnamed protein product|Mus musculus (10090)
Protein code \(c\) LZ-complexity \(\mathrm{LZ}(w)\) Length \(n=|w|\) \(\frac{\mathrm{LZ}(w)}{n /\log_{20} n}\) \(p_w(1)\) \(p_w(2)\) \(p_w(3)\) Sequence \(w=f(c)\)
1LSE , Knot 66 129 0.82 40 104 127 
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
1VYS , Knot 156 364 0.84 40 203 345 
SAEKLFTPLKVGAVTAPNRVFMAPLTRLRSIEPGDIPTPLMGEYYRQRASAGLIISEATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHAEDGRIAVQLYHTGRISHSSIQPGGQAPVSASALNANTRTSLRDENGNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVELHSAHGYLLHQFLSPSSNQRTDQYGGSVENRARLVLEVVDAVCNEWSADRIGIRVSPIGTFQNVDNGPNEEADALYLIEELAKRGIAYLHMSETDLAGGKPYSEAFRQKVRERFHGVIIGAGAYTAEKAEDLIGKGLIDAVAFGRDYIANPDLVARLQKKAELNPQRPESFYGGGAEGYTDYPSL
2DNA , Knot 35 67 0.73 38 50 58 
GSSGSSGPSHSLQAPEVRFSKEMECLQAMGFVNYNANLQALIATDGDTNAAIYKLKSSQGFSGPSSG

Let \(P_w(n)\) be the set of distinct subwords (intervals) in a word \(w\). Let \(p_w(n)\) be the cardinality of \(P_w(n)\). Let \(f(c)\) be the sequence in FASTA with 4-symbol Protein Data Bank code \(c\).

\(|P_{f(1LSE_1)}(2) \setminus P_{f(1VYS_1)}(2)|=39\), \(|P_{f(1VYS_1)}(2) \setminus P_{f(1LSE_1)}(2)|=138\). Let \( Z_k(x,y)=|P_x(k)\setminus P_y(k)|+|P_y(k)\setminus P_x(k)| \) be a LZ76 style (set of subwords) Jaccard distance numerator for \(P(k)\).Hydrophobic-polar version of Sequence 1:011100011111000110000100110110110100010001000000100001110100011000100110001001100111000101010010011001011011111000001001011101001
Pair \(Z_2\) Length of longest common subsequence
1LSE_1,1VYS_1 177 3
1LSE_1,2DNA_1 122 3
1VYS_1,2DNA_1 191 3

Newick tree

 
[
	1VYS_1:10.30,
	[
		1LSE_1:61,2DNA_1:61
	]:39.30
]

Let d be the Otu--Sayood distance d.
Let d1 be the Otu--Sayood distance d1. (This makes the 4TYN sequence AAAAAA a close match...)
A roughly speaking expected distance is \((0.85)(0.8)(\frac{493 }{\log_{20} 493}-\frac{129}{\log_{20}129})=107.\)
Status Protein1 Protein2 d d1/2
Query variables 1LSE_1 1VYS_1 136 91.5
Was not able to put for d
Was not able to put for d1

In notation analogous to [Theorem 16, Kjos-Hanssen, Niraula and Yoon (2022)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]