CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4JXF_1 4GJE_1 4WTG_1 Letter Amino acid
16 2 0 N Asparagine
12 11 0 D Aspartic acid
5 2 1 C Cysteine
17 4 0 I Isoleucine
17 6 0 K Lycine
10 5 0 F Phenylalanine
16 12 0 E Glutamic acid
33 6 0 L Leucine
14 7 0 V Valine
13 5 4 A Alanine
13 2 0 R Arginine
14 0 0 H Histidine
12 7 0 M Methionine
12 4 0 T Threonine
1 0 0 W Tryptophan
12 1 0 Y Tyrosine
6 4 0 Q Glutamine
15 6 0 G Glycine
10 2 0 P Proline
18 3 0 S Serine 

4JXF_1|Chain A|Serine/threonine-protein kinase PLK4|Homo sapiens (9606)
>4GJE_1|Chain A|Troponin C, slow skeletal and cardiac muscles|Homo sapiens (9606)
>4WTG_1|Chains A[auth P], B[auth T]|RNA PRIMER TEMPLATE CAAAAUUU|synthetic construct (32630)
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 \(w=f(c)\)
4JXF , Knot 121 266 0.84 40 177 260 
CIGEKIEDFKVGNLLGKGSFAGVYRAESIHTGLEVAIKMIDKKAMYKAGMVQRVQNEVKIHCQLKHPSILELYNYFEDSNYVYLVLEMCHNGEMNRYLKNRVKPFSENEARHFMHQIITGMLYLHSHGILHRDLTLSNLLLTRNMNIKIADFGLATQLKMPHEKHYTLCGTPNYISPEIATRSAHGLESDVWSLGCMFYTLLIGRPPFDTDTVKNTLNKVVLADYEMPSFLSIEAKDLIHQLLRRNPADRLSLSSVLDHPFMSRNS
4GJE , Knot 47 89 0.79 36 71 85 
MDDIYKAAVEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDS
4WTG , Knot 4 8 0.34 6 4 5 
CAAAAUUU

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 \(c\).

\(|P_{f(4JXF_1)}(2) \setminus P_{f(4GJE_1)}(2)|=140\), \(|P_{f(4GJE_1)}(2) \setminus P_{f(4JXF_1)}(2)|=34\). 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 1:01100100101101110101111001001001101110110001100111100100010100010010110100010000010111010001010001000101100001001100110111010001110001010011100010101101111001011000000101010010101100010110001101101100111101110000100010011110001101101010011001100011001010011001110000
Pair \(Z_2\) Length of longest common subsequence
4JXF_1,4GJE_1 174 3
4JXF_1,4WTG_1 181 1
4GJE_1,4WTG_1 73 2

Newick tree

 
[
	4JXF_1:10.30,
	[
		4GJE_1:36.5,4WTG_1:36.5
	]:63.80
]

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 \((0.85)(0.8)(\frac{355 }{\log_{20} 355}-\frac{89}{\log_{20}89})=82.7\)
Status Protein1 Protein2 d d1/2
Query variables 4JXF_1 4GJE_1 105 68.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]