CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2GIY_1 7MRZ_1 5LLC_1 Letter Amino acid
11 5 7 R Arginine
5 5 10 N Asparagine
7 9 1 C Cysteine
9 8 22 G Glycine
11 5 26 L Leucine
15 8 17 P Proline
17 7 18 S Serine
11 4 12 T Threonine
8 6 19 D Aspartic acid
6 6 11 Q Glutamine
15 3 12 H Histidine
0 6 24 K Lycine
4 5 2 M Methionine
7 7 8 Y Tyrosine
16 4 17 V Valine
8 6 9 I Isoleucine
21 5 13 A Alanine
12 4 13 E Glutamic acid
4 4 12 F Phenylalanine
4 2 7 W Tryptophan 

2GIY_1|Chains A, B|Glycoprotein E|Human herpesvirus 1 (10306)
>7MRZ_1|Chain A|Growth/differentiation factor 11|Homo sapiens (9606)
>5LLC_1|Chain A|Carbonic anhydrase 2|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 \(w=f(c)\)
2GIY , Knot 91 191 0.83 38 139 184 
GAPEVSHVRGVTVRMETPEAILFSPGETFSTNVSIHAIAHDDQTYSMDVVWLRFDVPTSCAEMRIYESCLYHPQLPECLSPADAPCAASTWTSRLAVRSYAGCSRTNPPPRCSAEAHMEPVPGLAWQAASVNLEFRDASPQHSGLYLCVVYVNDHIHAWGHITISTAAQYRNAVVEQPLDIEGRGHHHHHH
7MRZ , Knot 58 109 0.83 40 99 107 
NLGLDCDEHSSESRCCRYPLTVDFEAFGWDWIIAPKRYKANYCSGQCEYMFMQKYPHTHLVQQANPRGSAGPCCTPTKMSPINMLYFNDKQQIIYGKIPGMVVDRCGCS
5LLC , Knot 112 260 0.79 40 176 249 
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK

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 \(c\).

\(|P_{f(2GIY_1)}(2) \setminus P_{f(7MRZ_1)}(2)|=109\), \(|P_{f(7MRZ_1)}(2) \setminus P_{f(2GIY_1)}(2)|=69\). 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 1:11101001011010100101111011001000101011100000001011110101100010101000010010110010110110110010001110001100000111000101010111111101101010100101000110101101000101110101001100001110011010101000000
Pair \(Z_2\) Length of longest common subsequence
2GIY_1,7MRZ_1 178 3
2GIY_1,5LLC_1 181 3
7MRZ_1,5LLC_1 183 3

Newick tree

 
[
	5LLC_1:91.65,
	[
		2GIY_1:89,7MRZ_1:89
	]:2.65
]

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 \((0.85)(0.8)(\frac{300 }{\log_{20} 300}-\frac{109}{\log_{20}109})=59.8\)
Status Protein1 Protein2 d d1/2
Query variables 2GIY_1 7MRZ_1 78 61
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]