CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2EHG_1 8WDM_1 8FJX_1 Letter Amino acid
4 8 3 M Methionine
6 38 7 P Proline
7 13 1 Y Tyrosine
9 48 8 R Arginine
5 27 9 D Aspartic acid
14 2 12 K Lycine
16 48 19 L Leucine
4 20 7 F Phenylalanine
13 62 15 G Glycine
0 14 11 H Histidine
18 13 16 I Isoleucine
5 18 10 T Threonine
8 11 9 N Asparagine
3 3 3 C Cysteine
12 31 14 E Glutamic acid
1 13 2 W Tryptophan
7 48 21 V Valine
8 82 21 A Alanine
2 11 8 Q Glutamine
7 17 14 S Serine 

2EHG_1|Chain A|ribonuclease HI|Sulfolobus tokodaii (273063)
>8WDM_1|Chains A, B, C, D|Carboxylic ester hydrolase|Thermaerobacter marianensis (strain ATCC 700841 / DSM 12885 / JCM 10246 / 7p75a) (644966)
>8FJX_1|Chain A|Trifunctional purine biosynthetic protein adenosine-3|Homo sapiens (9606)
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 \(w=f(c)\)
2EHG , Knot 77 149 0.86 38 123 147 
MIIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPREENKEADRLSRVAYELVRRGKLRDIGCIILT
8WDM , Knot 197 527 0.78 40 204 446 
MHHHHHHENLYFQGAGAGAGAGAMATARELHDVIVETRYGAVRGRSDGTVCVWKGVPFARPPVGPLRFRPPEPPEPWSGVRDATRFGPASVQPEDRLISNLTGGATLPQDEDCLYLNIWSPSPDGRRPVMVWIHGGAYLTGAGSIPWYDGTALAREGDVVVVTLNYRLGALGFLYLEDAFGPEFTGSGNLGILDQIAALRWVRENIAAFGGDPDRVTIFGESAGAGSVGVLLAAPAARGLFHRAILQSGSGALGVRTAASAARVAARVLQHAGVEPGDREALRSLPARAWANAVAALGPGLPLGPVVDGTVLPEHPMAALARGAARDVAVLVGVNKDEYNLFALQDPAWLGDDEAALRQRVEAVVGPAAGRLIEFYRSRGEGSLGRRLLPLMSYAVFVRGMLATADAQARVGAPVWAYRFDFETPVLGGVLGACHALEIPFVFNTLDRAGADRFTGTAPERYAVAQAMHRAWIAFAREGNPQHDGLPEWPRYDLEERAVMVFAVEPRVERDPWRAEREVWAAAGVGA
8FJX , Knot 93 210 0.79 40 139 199 
MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH

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 \(c\).

\(|P_{f(2EHG_1)}(2) \setminus P_{f(8WDM_1)}(2)|=54\), \(|P_{f(8WDM_1)}(2) \setminus P_{f(2EHG_1)}(2)|=135\). 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 1:11110101100100111110111110100001010111001101000001100011101100110111001110100011100101000101001111000110100010101111100000010010011001100101001101110
Pair \(Z_2\) Length of longest common subsequence
2EHG_1,8WDM_1 189 3
2EHG_1,8FJX_1 132 3
8WDM_1,8FJX_1 163 6

Newick tree

 
[
	8WDM_1:94.49,
	[
		2EHG_1:66,8FJX_1:66
	]:28.49
]

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 \((0.85)(0.8)(\frac{676 }{\log_{20} 676}-\frac{149}{\log_{20}149})=150.\)
Status Protein1 Protein2 d d1/2
Query variables 2EHG_1 8WDM_1 177 116
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]