CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1RNX_1 6XIB_1 6GUW_1 Letter Amino acid
4 8 7 R Arginine
10 5 8 K Lycine
4 5 5 P Proline
4 1 6 M Methionine
3 4 9 F Phenylalanine
15 6 13 S Serine
10 7 6 T Threonine
12 11 11 A Alanine
10 0 3 N Asparagine
5 8 6 D Aspartic acid
7 5 8 Q Glutamine
0 1 1 W Tryptophan
6 4 4 Y Tyrosine
9 8 11 V Valine
5 14 15 E Glutamic acid
3 8 8 G Glycine
4 6 10 H Histidine
3 2 7 I Isoleucine
8 1 5 C Cysteine
2 18 12 L Leucine 

1RNX_1|Chain A|RIBONUCLEASE A|Bos taurus (9913)
>6XIB_1|Chain A|Proprotein convertase subtilisin/kexin type 9|Homo sapiens (9606)
>6GUW_1|Chain A|POZ (BTB) and AT hook-containing zinc finger 1|Danio rerio (7955)
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 \(w=f(c)\)
1RNX , Knot 64 124 0.83 38 107 121 
KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV
6XIB , Knot 58 122 0.76 38 87 115 
QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ
6GUW , Knot 77 155 0.83 40 124 149 
MAHHHHHHSAALEVLFQGPGMERTEQPWNSSYTYQVSKHSAEMLHNLNGQRKDGGRFCDVILRVGEESFPAHKAVLAACSEYFESVFSCQTEDDGQGKELEMHTISPKVFRDILDFAYTSKIVVRLECFPELMTAAKFLLMRSVIEICQEVIKQS

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 \(c\).

\(|P_{f(1RNX_1)}(2) \setminus P_{f(6XIB_1)}(2)|=85\), \(|P_{f(6XIB_1)}(2) \setminus P_{f(1RNX_1)}(2)|=65\). 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 1:0001110100001000001100000000110000100000011001100011010110000011000100000000001010000001000010010000010001111001010111010101
Pair \(Z_2\) Length of longest common subsequence
1RNX_1,6XIB_1 150 3
1RNX_1,6GUW_1 173 4
6XIB_1,6GUW_1 137 3

Newick tree

 
[
	1RNX_1:84.69,
	[
		6XIB_1:68.5,6GUW_1:68.5
	]:16.19
]

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 \((0.85)(0.8)(\frac{246 }{\log_{20} 246}-\frac{122}{\log_{20}122})=39.2\)
Status Protein1 Protein2 d d1/2
Query variables 1RNX_1 6XIB_1 52 51
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]