CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4LMD_1 2HAP_1 7NSJ_1 Letter Amino acid
11 0 16 L Leucine
11 0 13 K Lycine
6 8 8 T Threonine
7 0 6 Y Tyrosine
10 0 16 V Valine
5 0 8 R Arginine
1 0 3 M Methionine
12 0 4 F Phenylalanine
8 5 19 A Alanine
4 0 1 D Aspartic acid
5 0 3 Q Glutamine
8 0 6 E Glutamic acid
6 0 2 I Isoleucine
5 0 9 P Proline
6 0 5 N Asparagine
4 4 1 C Cysteine
7 3 14 G Glycine
6 0 6 H Histidine
10 0 7 S Serine
0 0 1 W Tryptophan 

4LMD_1|Chains A, B|Large T antigen|JC polyomavirus (10632)
>2HAP_1|Chain A|DNA (5'-D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3')|null
>7NSJ_1|Chain A[auth B0]|Mitochondrial ribosomal protein L27|Sus scrofa (9823)
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 \(w=f(c)\)
4LMD , Knot 67 132 0.82 38 110 130 
GSKVEDPKDFPVDLHAFLSQAVFSNRTVASFAVYTTKEKAQILYKKLMEKYSVTFISRHGFGGHNILFFLTPHRHRVSAINNYCQKLCTFSFLICKGVNKEYLFYSALCRQPYAVVEESIQGGLKEHDFNPE
2HAP , Knot 8 20 0.40 8 10 11 
ACGCTATTATCGCTATTAGT
7NSJ , Knot 68 148 0.76 40 106 142 
MALAVLALRTRAAVTALLSPPQAAALAVRYASKKTGGSSKNLGGKSPGKRFGIKKMEGHYVHAGNILATQRHFRWHPGAHVGLGKNKCLYALEEGVVRYTKEVYVPNPSNSEAVDLVTRLPQGAVLYKTFVHVVPAKPEGTFKLVAML

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 \(c\).

\(|P_{f(4LMD_1)}(2) \setminus P_{f(2HAP_1)}(2)|=108\), \(|P_{f(2HAP_1)}(2) \setminus P_{f(4LMD_1)}(2)|=8\). 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 1:100100100111010111001110000110111000000101100011000010110001111001111101000010110000001001011100110000110011000101110001011100001010
Pair \(Z_2\) Length of longest common subsequence
4LMD_1,2HAP_1 116 2
4LMD_1,7NSJ_1 138 3
2HAP_1,7NSJ_1 108 2

Newick tree

 
[
	4LMD_1:66.66,
	[
		2HAP_1:54,7NSJ_1:54
	]:12.66
]

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 \((0.85)(0.8)(\frac{152 }{\log_{20} 152}-\frac{20}{\log_{20}20})=48.0\)
Status Protein1 Protein2 d d1/2
Query variables 4LMD_1 2HAP_1 66 36.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]