CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6TNC_1 6MWX_1 3IDY_1 Letter Amino acid
10 41 12 A Alanine
19 19 9 D Aspartic acid
19 13 12 Q Glutamine
9 14 5 H Histidine
11 36 25 T Threonine
15 20 18 E Glutamic acid
29 25 18 K Lycine
16 38 21 V Valine
16 16 31 N Asparagine
14 30 24 G Glycine
22 22 19 L Leucine
14 29 13 P Proline
24 36 26 S Serine
4 6 8 W Tryptophan
7 11 10 R Arginine
5 16 18 C Cysteine
31 26 24 I Isoleucine
9 4 6 M Methionine
5 19 13 F Phenylalanine
15 20 5 Y Tyrosine 

6TNC_1|Chain A|Dual specificity protein kinase TTK|Homo sapiens (9606)
>6MWX_1|Chains A, E, I, M|E1|Eastern equine encephalitis virus (11021)
>3IDY_1|Chains A, D[auth G]|HIV-1 HxBc2 gp120 core|Human immunodeficiency virus 1 (11676)
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 \(w=f(c)\)
6TNC , Knot 133 294 0.85 40 188 284 
GSNECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTT
6MWX , Knot 186 441 0.85 40 229 415 
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVVKCCGATQCTSKPHPDYQCQVFTGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAKAYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVVYGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQAPSGFERWKRDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDLECKITECTYASDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTANIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWLKVLVGGTSAFIVLGLIATAVVALVLFFHRH
3IDY , Knot 134 317 0.81 40 188 293 
EVVLVNVTENFNWCKNDMVEQMHEDICSLWDQSLKPCVKLTPLCVGAGSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSSQLLLNGSLAEEEVVIRSCNFTDNAKTIIVQLNTSVEINCTGAGHCNIARAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHWFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWCKVGKMMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE

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 \(c\).

\(|P_{f(6TNC_1)}(2) \setminus P_{f(6MWX_1)}(2)|=65\), \(|P_{f(6MWX_1)}(2) \setminus P_{f(6TNC_1)}(2)|=106\). 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 1:100001010101001100110110001101100000101100101001000010000001101001000000110100001000010111001010100110000010110000010011011001000111000101101111011101101111001010000110000110100111011001000000100000101000110110110010010011001100100101110100010110110001001100010001000101101110101010001100110100
Pair \(Z_2\) Length of longest common subsequence
6TNC_1,6MWX_1 171 4
6TNC_1,3IDY_1 194 4
6MWX_1,3IDY_1 173 3

Newick tree

 
[
	3IDY_1:93.93,
	[
		6TNC_1:85.5,6MWX_1:85.5
	]:8.43
]

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 \((0.85)(0.8)(\frac{735 }{\log_{20} 735}-\frac{294}{\log_{20}294})=121.\)
Status Protein1 Protein2 d d1/2
Query variables 6TNC_1 6MWX_1 155 129
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]