CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1MWK_1 8TYC_1 1WJK_1 Letter Amino acid
21 19 6 G Glycine
6 10 2 H Histidine
26 18 3 I Isoleucine
30 32 13 L Leucine
3 3 1 W Tryptophan
11 7 5 R Arginine
23 19 5 N Asparagine
24 8 4 D Aspartic acid
18 10 6 E Glutamic acid
10 10 5 F Phenylalanine
2 10 2 C Cysteine
22 7 7 K Lycine
6 11 2 M Methionine
25 21 11 S Serine
21 20 5 T Threonine
12 13 3 Y Tyrosine
25 14 5 V Valine
15 12 4 A Alanine
12 10 4 Q Glutamine
8 5 7 P Proline 

1MWK_1|Chains A, B|ParM|Escherichia coli (562)
>8TYC_1|Chains A, B, C|Glycoprotein G1|Lassa virus (11622)
>1WJK_1|Chain A|C330018D20rik protein|Mus musculus (10090)
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 \(w=f(c)\)
1MWK , Knot 140 320 0.84 40 188 307 
MLVFIDDGSTNIKLQWQESDGTIKQHISPNSFKREWAVSFGDKKVFNYTLNGEQYSFDPISPDAVVTTNIAWQYSDVNVVAVHHALLTSGLPVSEVDIVCTLPLTEYYDRNNQPNTENIERKKANFRKKITLNGGDTFTIKDVKVMPESIPAGYEVLQELDELDSLLIIDLGGTTLDISQVMGKLSGISKIYGDSSLGVSLVTSAVKDALSLARTKGSSYLADDIIIHRKDNNYLKQRINDENKISIVTEAMNEALRKLEQRVLNTLNEFSGYTHVMVIGGGAELICDAVKKHTQIRDERFFKTNNSQYDLVNGMYLIGN
8TYC , Knot 116 259 0.83 40 171 248 
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIGYLGLLSQRTRDIYISRRLL
1WJK , Knot 52 100 0.79 40 83 95 
GSSGSSGNLSASNRALPVLTLFTKAPCPLCDEAKEVLQPYKDRFILQEVDITLPENSTWYERYKFDIPVFHLNGQFLMMHRVNTSKLEKQLRKLSGPSSG

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 \(c\).

\(|P_{f(1MWK_1)}(2) \setminus P_{f(8TYC_1)}(2)|=92\), \(|P_{f(8TYC_1)}(2) \setminus P_{f(1MWK_1)}(2)|=75\). 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 1:11111001000101010000101000101001000111011000110001010000101101011100011100001011110011100111100101100111000000000100001000010100010101100101001011100111100110010010011110111001010011101011001010001110110011001101100010001100111000000010001000001011001100110010001100100101000111111110110011000001000011000000001101101110
Pair \(Z_2\) Length of longest common subsequence
1MWK_1,8TYC_1 167 3
1MWK_1,1WJK_1 167 4
8TYC_1,1WJK_1 180 3

Newick tree

 
[
	1WJK_1:87.88,
	[
		1MWK_1:83.5,8TYC_1:83.5
	]:4.38
]

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 \((0.85)(0.8)(\frac{579 }{\log_{20} 579}-\frac{259}{\log_{20}259})=90.4\)
Status Protein1 Protein2 d d1/2
Query variables 1MWK_1 8TYC_1 114 102
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]