CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8AHB_1 5FLX_1 8DOX_1 Letter Amino acid
19 6 17 D Aspartic acid
7 6 13 Q Glutamine
15 4 7 H Histidine
22 17 29 L Leucine
7 1 10 M Methionine
12 10 16 S Serine
16 9 23 T Threonine
8 11 17 A Alanine
23 17 27 G Glycine
11 7 13 P Proline
1 3 3 W Tryptophan
7 23 11 R Arginine
21 31 11 K Lycine
12 3 16 F Phenylalanine
12 12 11 I Isoleucine
2 5 12 C Cysteine
16 14 9 E Glutamic acid
11 10 11 Y Tyrosine
17 9 26 V Valine
13 10 21 N Asparagine 

8AHB_1|Chain A|Green fluorescent protein|Aequorea victoria (6100)
>5FLX_10|Chain J[auth I]|40S RIBOSOMAL PROTEIN S8|ORYCTOLAGUS CUNICULUS (9986)
>8DOX_1|Chain A|3C-like proteinase nsp5|Severe acute respiratory syndrome coronavirus 2 (2697049)
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 \(w=f(c)\)
8AHB , Knot 111 252 0.81 40 163 237 
MRGSHHHHHHTDPMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLAYGVLCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKSNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYK
5FLX , Knot 97 208 0.83 40 139 198 
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK
8DOX , Knot 133 303 0.83 40 195 288 
GSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSG

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 \(c\).

\(|P_{f(8AHB_1)}(2) \setminus P_{f(5FLX_1)}(2)|=95\), \(|P_{f(5FLX_1)}(2) \setminus P_{f(8AHB_1)}(2)|=71\). 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 1:101000000000111001001101111111010101010010101010101001010101100010111111011001101110100010010000110011101010000111000100000101010100110010101101000101110010000000010111000001100010100010010101100000001110111111000010000010001000000111101101111011100100
Pair \(Z_2\) Length of longest common subsequence
8AHB_1,5FLX_1 166 3
8AHB_1,8DOX_1 168 3
5FLX_1,8DOX_1 192 4

Newick tree

 
[
	8DOX_1:92.47,
	[
		8AHB_1:83,5FLX_1:83
	]:9.47
]

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 \((0.85)(0.8)(\frac{460 }{\log_{20} 460}-\frac{208}{\log_{20}208})=73.4\)
Status Protein1 Protein2 d d1/2
Query variables 8AHB_1 5FLX_1 96 87.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]