CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8ADC_1 3UVI_1 8HCF_1 Letter Amino acid
13 8 4 N Asparagine
16 24 11 D Aspartic acid
2 10 13 H Histidine
13 33 22 S Serine
18 38 20 A Alanine
3 18 14 Q Glutamine
13 34 16 G Glycine
11 17 22 P Proline
1 3 3 W Tryptophan
12 18 11 V Valine
7 32 14 R Arginine
4 3 7 C Cysteine
20 24 12 E Glutamic acid
16 14 7 K Lycine
12 18 19 T Threonine
8 8 5 Y Tyrosine
12 22 8 I Isoleucine
17 27 33 L Leucine
7 17 3 M Methionine
10 20 6 F Phenylalanine 

8ADC_1|Chains A, B|Deubiquitinating enzyme|Waddlia chondrophila (71667)
>3UVI_1|Chain A|Queuine tRNA-ribosyltransferase|Zymomonas mobilis (542)
>8HCF_1|Chains A, B|Three-prime repair exonuclease 1|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 \(w=f(c)\)
8ADC , Knot 100 215 0.83 40 163 212 
KMPEEEQDSLAAFSRIEANITQYDPLLDNAGKSACTCICLKAAEMLLEASPDQVNAGLIDDILVEGVADYNRFKVGGVVEHTSVENYELNTFELKRLEFRDVDNPFSAEGNPYAGTLDSFAKMMEKASDSKDLPKPVALVMTKSNMTITIVIRPDGKYWLFDPHGTNGKGAYIESCNTDELIKKIKEIFPKTSYPGMTEDENLGFNSFEAYAVRR
3UVI , Knot 162 388 0.83 40 213 373 
GSMVEATAQETDRPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMSLSSLTKQSEEGVTFKSHLDGSRHMLSPERSIEIQHLLGSDIVMAFDESTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDSVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPLDSECHCAVCQKESRAYIHHLIRAGQILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYFARNS
8HCF , Knot 111 250 0.81 40 159 240 
MGSQTLPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGTPATTGTTLEHHHHHH

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 \(c\).

\(|P_{f(8ADC_1)}(2) \setminus P_{f(3UVI_1)}(2)|=61\), \(|P_{f(3UVI_1)}(2) \setminus P_{f(8ADC_1)}(2)|=111\). 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 1:01100000011110010101000011100110010001010110111010100101111001110111000010111110000100001001010010100100110101010110100110110010000011011111100001010111010100111010100101101000000011001001110000111000001110010101100
Pair \(Z_2\) Length of longest common subsequence
8ADC_1,3UVI_1 172 3
8ADC_1,8HCF_1 168 3
3UVI_1,8HCF_1 176 4

Newick tree

 
[
	3UVI_1:87.98,
	[
		8ADC_1:84,8HCF_1:84
	]:3.98
]

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 \((0.85)(0.8)(\frac{603 }{\log_{20} 603}-\frac{215}{\log_{20}215})=110.\)
Status Protein1 Protein2 d d1/2
Query variables 8ADC_1 3UVI_1 138 108
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]