CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2JRQ_1 8UMG_1 2GPE_1 Letter Amino acid
0 7 4 R Arginine
1 8 1 N Asparagine
0 11 4 D Aspartic acid
0 10 1 H Histidine
0 11 4 I Isoleucine
0 11 1 Y Tyrosine
6 5 0 C Cysteine
0 11 2 Q Glutamine
4 12 2 G Glycine
0 3 2 M Methionine
0 6 1 W Tryptophan
0 4 1 V Valine
4 11 4 A Alanine
0 19 4 E Glutamic acid
0 5 1 F Phenylalanine
0 8 3 S Serine
0 10 7 T Threonine
0 8 5 L Leucine
0 22 3 K Lycine
0 5 2 P Proline 

2JRQ_1|Chain A|5'-R(*CP*CP*UP*CP*CP*CP*UP*(CM0)P*AP*CP*AP*AP*GP*GP*AP*GP*G)-3'|
>8UMG_1|Chains A, B, C|Chromodomain-helicase-DNA-binding protein 1|Homo sapiens (9606)
>2GPE_1|Chains A, B, C, D|Bifunctional protein putA|Escherichia coli (562)
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 \(w=f(c)\)
2JRQ , Knot 9 17 0.50 10 11 13 
CCUCCCUNACAAGGAGG
8UMG , Knot 87 187 0.81 40 145 180 
MKKHHHHHHEEEFETIERFMDCRIGRKGATGATTTIYAVEADGDPNAGFEKNKEPGEIQYLIKWKGWSHIHNTWETEETLKQQNVRGMKKLDNYKKKDQETKRWLKNASPEDVEYYNCQQELTDDLHKQYQIVGRIIAHSNQKSAAGYPDYYCKWQGLPYSECSWEDGALISKKFQACIDEYFSRKK
2GPE , Knot 30 52 0.76 38 44 49 
MGTTTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLENSDTLPE

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 \(c\).

\(|P_{f(2JRQ_1)}(2) \setminus P_{f(8UMG_1)}(2)|=6\), \(|P_{f(8UMG_1)}(2) \setminus P_{f(2JRQ_1)}(2)|=140\). 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 1:00000000101111111
Pair \(Z_2\) Length of longest common subsequence
2JRQ_1,8UMG_1 146 3
2JRQ_1,2GPE_1 53 2
8UMG_1,2GPE_1 147 4

Newick tree

 
[
	8UMG_1:83.18,
	[
		2JRQ_1:26.5,2GPE_1:26.5
	]:56.68
]

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 \((0.85)(0.8)(\frac{204 }{\log_{20} 204}-\frac{17}{\log_{20}17})=65.9\)
Status Protein1 Protein2 d d1/2
Query variables 2JRQ_1 8UMG_1 81 43.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: