CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8ZUP_1 3OGK_1 7PXL_1 Letter Amino acid
17 13 16 D Aspartic acid
2 3 2 C Cysteine
8 4 8 Q Glutamine
14 20 5 E Glutamic acid
10 2 8 H Histidine
19 13 3 K Lycine
3 4 1 M Methionine
9 19 22 A Alanine
1 2 6 W Tryptophan
21 4 18 G Glycine
12 6 6 F Phenylalanine
7 4 7 R Arginine
18 12 11 L Leucine
10 4 20 P Proline
12 8 20 S Serine
15 10 16 T Threonine
10 2 10 Y Tyrosine
17 12 23 V Valine
12 10 16 I Isoleucine
13 8 17 N Asparagine 

8ZUP_1|Chain A|Green fluorescent protein|Aequorea victoria (6100)
>3OGK_1|Chains A, D[auth C], G[auth E], J[auth G], L[auth I], O[auth K], R[auth M], U[auth O]|SKP1-like protein 1A|Arabidopsis thaliana (3702)
>7PXL_1|Chain A|Auxiliary activity 9|Lentinus similis (292560)
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 \(w=f(c)\)
8ZUP , Knot 105 230 0.82 40 154 218 
SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSVQSALSKDPNEKRDHMVLLQFVTAAGITH
3OGK , Knot 78 160 0.82 40 117 150 
MSAKKIVLKSSDGESFEVEEAVALESQTIAHMVEDDCVDNGVPLPNVTSKILAKVIEYCKRHVEAAASKAEAVEGAATSDDDLKAWDADFMKIDQATLFELILAANYLNIKNLLDLTCQTVADMIKGKTPEEIRTTFNIKNDFTPEEEEEVRRENQWAFE
7PXL , Knot 105 235 0.81 40 154 226 
HTLVWGVWVNGVDQGDGRNIYIRSPPNNNPVKNLTSPDMTCNVDNRVVPKSVPVNAGDTLTFEWYHNTRDDDIIASSHHGPIAVYIAPAASNGQGNVWVKLFEDAYNVTNSTWAVDRLITAHGQHSVVVPHVAPGDYLFRAEIIALHEADSLYSQNPIRGAQFYISCAQITINSSDDSTPLPAGVPFPGAYTDSTPGIQFNIYTTPATSYVAPPPSVWSGALGGSIAQVGDASLE

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 \(c\).

\(|P_{f(8ZUP_1)}(2) \setminus P_{f(3OGK_1)}(2)|=88\), \(|P_{f(3OGK_1)}(2) \setminus P_{f(8ZUP_1)}(2)|=51\). 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 1:00100110111111101010101001010101010100101010110001011111101100100110010001001000011001110101000010100010000010101010011001010110100010111001000000001010100000110101010001001010110000000111011111100001010011000100000011110110111100
Pair \(Z_2\) Length of longest common subsequence
8ZUP_1,3OGK_1 139 3
8ZUP_1,7PXL_1 174 4
3OGK_1,7PXL_1 165 3

Newick tree

 
[
	7PXL_1:89.29,
	[
		8ZUP_1:69.5,3OGK_1:69.5
	]:19.79
]

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 \((0.85)(0.8)(\frac{390 }{\log_{20} 390}-\frac{160}{\log_{20}160})=68.9\)
Status Protein1 Protein2 d d1/2
Query variables 8ZUP_1 3OGK_1 87 73
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]