CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6QYA_1 7UWH_1 6JVY_1 Letter Amino acid
31 0 6 L Leucine
20 0 5 F Phenylalanine
6 0 0 W Tryptophan
22 10 11 A Alanine
12 0 3 N Asparagine
3 21 1 C Cysteine
15 0 5 P Proline
13 0 10 S Serine
14 0 5 Q Glutamine
12 0 8 H Histidine
17 0 7 K Lycine
8 0 5 M Methionine
15 12 10 T Threonine
13 0 9 R Arginine
21 0 7 D Aspartic acid
27 0 4 E Glutamic acid
20 16 17 G Glycine
15 0 5 I Isoleucine
14 0 4 Y Tyrosine
17 0 6 V Valine

6QYA_1|Chains A, C|Thymidylate synthase|Enterococcus faecalis (1351)
>7UWH_1|Chain A|DNA (59-MER)|Escherichia coli (562)
>6JVY_1|Chain A|RNA-binding protein 38|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 \(w=f(c)\)
6QYA , Knot 142 315 0.86 40 209 306
MEEAYLALGKKILEEGHFKEDRTGTGTYSLFGYQMRFDLAKGFPLLTTKRVPFGLIKSELLWFLKGDTNIRYLLERNNHIWDEWAFERYVKSADYQGPDMTDFGHRVLQDPAFAEQYKEEHQKFCDAILNDAEFAEKYGELGNIYGAQWRHWETKDGSFIDQLANVIEMIKTNPDSRRLIVSAWNPEDVPSMALPPCHTMFQFYVNEGKLSCQLYQRSADVFLGVPFNIASYALLTHLIAHETGLEVGEFVHTLGDAHLYQNHVEQMQEQLSREVRSFPTLVLNPDKASVFDFDMEDIKVEGYDPHPTIKAPIAV
7UWH , Knot 22 59 0.50 8 15 36
GCCGTAGGCGGGCTACCTCTCCATGACGGCGAATACCCTCCCAGGCCTGCTGGTAATCT
6JVY , Knot 65 128 0.82 38 97 121
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTG

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 \(c\).

\(|P_{f(6QYA_1)}(2) \setminus P_{f(7UWH_1)}(2)|=206\), \(|P_{f(7UWH_1)}(2) \setminus P_{f(6QYA_1)}(2)|=12\). 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 1:100101111001100101000001010001110010101101111100001111110001111101000100110000011001110001001000110100110011001111000000000100111001011000101101011010010000101100110110110001000011101101001101111100011010100101000100001011111110110011100111000110110110011010100001001000100010011011101001011010100101010010101011111
Pair \(Z_2\) Length of longest common subsequence
6QYA_1,7UWH_1 218 2
6QYA_1,6JVY_1 182 3
7UWH_1,6JVY_1 102 3

Newick tree

 
[
	6QYA_1:11.13,
	[
		6JVY_1:51,7UWH_1:51
	]:61.13
]

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 \((0.85)(0.8)(\frac{374 }{\log_{20} 374}-\frac{59}{\log_{20}59})=99.1\)
Status Protein1 Protein2 d d1/2
Query variables 6QYA_1 7UWH_1 139 79.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]