CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8QGZ_1 5DMP_1 1EHT_1 Letter Amino acid
6 6 0 H Histidine
3 6 0 M Methionine
12 8 0 S Serine
7 8 7 A Alanine
7 9 0 D Aspartic acid
7 4 0 Q Glutamine
10 9 0 V Valine
4 1 0 N Asparagine
14 20 11 G Glycine
7 8 0 Y Tyrosine
7 8 0 R Arginine
2 0 11 C Cysteine
5 17 0 E Glutamic acid
3 4 0 F Phenylalanine
5 10 0 P Proline
8 8 0 T Threonine
3 3 0 W Tryptophan
4 12 0 I Isoleucine
10 12 0 L Leucine
5 16 0 K Lycine 

8QGZ_1|Chains A, B, C, D|NbE201|Lama glama (9844)
>5DMP_1|Chain A|Uncharacterized protein|Methanocella paludicola (570267)
>1EHT_1|Chain A|THEOPHYLLINE-BINDING RNA|
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 \(w=f(c)\)
8QGZ , Knot 64 129 0.80 40 106 123 
QVQLQESGGGLVQAGGSLRLSCVVPGRTISLYRMGWFRQAPGKEREFVAGINWSGDMTDYVDSVKGRFTISRDNAKNTVYLEMNSLKPEDTAIYYCTADPKLLPLADSSYGYWGQGTQVTVSSHHHHHH
5DMP , Knot 80 169 0.81 38 127 162 
IKHPIYVIQKHDASHLHYDLRLEMGGVLKSWAVPKGPSLDPKVKRLAMPTEDHPIGYATFEGVIPEGQYGGGTVMVWDIGTYRNLREEKPEGSRMTIEQSYDQGKIEVFLEGKKLKGSYALIRTGGIEKRGWLFFKMKEPHEGSYEDIEKAAPDSVLTGRTMDEIAKEG
1EHT , Knot 14 33 0.49 8 16 24 
GGCGAUACCAGCCGAAAGGCCCUUGGCAGCGUC

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 \(c\).

\(|P_{f(8QGZ_1)}(2) \setminus P_{f(5DMP_1)}(2)|=61\), \(|P_{f(5DMP_1)}(2) \setminus P_{f(8QGZ_1)}(2)|=82\). 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 1:010100011111011101010011110010100111100111000011111010101000100101010100001000101010010100011000010101111100001011010010100000000
Pair \(Z_2\) Length of longest common subsequence
8QGZ_1,5DMP_1 143 3
8QGZ_1,1EHT_1 118 3
5DMP_1,1EHT_1 139 2

Newick tree

 
[
	5DMP_1:73.94,
	[
		8QGZ_1:59,1EHT_1:59
	]:14.94
]

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 \((0.85)(0.8)(\frac{298 }{\log_{20} 298}-\frac{129}{\log_{20}129})=52.4\)
Status Protein1 Protein2 d d1/2
Query variables 8QGZ_1 5DMP_1 67 58
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]