CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8CQN_1 3SUR_1 8GAT_1 Letter Amino acid
5 12 6 M Methionine
0 10 13 W Tryptophan
11 17 24 R Arginine
32 27 27 N Asparagine
13 30 24 D Aspartic acid
25 32 27 I Isoleucine
8 35 37 V Valine
18 42 17 A Alanine
0 2 19 C Cysteine
9 19 13 Q Glutamine
8 25 15 P Proline
6 25 14 Y Tyrosine
2 15 14 H Histidine
26 34 28 L Leucine
38 27 27 K Lycine
23 48 48 S Serine
32 25 27 E Glutamic acid
5 46 45 G Glycine
7 17 15 F Phenylalanine
7 37 26 T Threonine 

8CQN_1|Chains A, B|Lipoprotein, putative|Borreliella burgdorferi B31 (224326)
>3SUR_1|Chain A|Beta-hexosaminidase|Paenibacillus (192895)
>8GAT_1|Chain A|Vasodilator-stimulated phosphoprotein, Neuraminidase chimera|Homo sapiens (9606)
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 \(w=f(c)\)
8CQN , Knot 116 275 0.79 36 152 253 
GAMGNKEQKNNNNVKEVSDSVQEDGLNDLYNNQEKQKSFTKNFGERKYEDLINPIEPIIPSESPKNKANIPNISIAHTEKKETKKENLIPSTNEEKEADAAIKYLEENILKNSKFSELIREVRVIKDEYALIKADLYDVIGKINNKKTSLMENPKNNRDKINKLTQLLQNNLKIDSELEQLINMIDMAENEISSAAFFFDNAQKRLKESIIKRLESKNNRSYALKLSRQALSDARSALSNLESFASKRIEPMVRKEEIKELIKHAKTVLESLNKK
3SUR , Knot 209 525 0.83 40 248 488 
MGSSHHHHHHSSGLVPRGSHMASMMSFIPESASASTSQPSILPKPVSYTVGSGQFVLTKNASIFVAGNNVGETDELFNIGQALAKKLNASTGYTISVVKSNQPTAGSIYLTTVGGNAALGNEGYDLITTSNQVTLTANKPEGVFRGNQTLLQLLPAGIEKNTVVSGVQWVIPHSNISDKPEYEYRGLMLDVARHFFTVDEVKRQIDLASQYKINKFHMHLSDDQGWRIEIKSWPDLIEIGSKGQVGGGPGGYYTQEQFKDIVSYAAERYIEVIPEIDMPGHTNAALASYGELNPDGKRKAMRTDTAVGYSTLMPRAEITYQFVEDVISELAAISPSPYIHLGGDESNATSAADYDYFFGRVTAIANSYGKKVVGWDPSDTSSGATSDSVLQNWTCSASTGTAAKAKGMKVIVSPANAYLDMKYYSDSPIGLQWRGFVNTNRAYNWDPTDCIKGANIYGVESTLWTETFVTQDHLDYMLYPKLLSNAEVGWTARGDRNWDDFKERLIEHTPRLQNKGIKFFADPIV
8GAT , Knot 192 466 0.84 40 244 436 
MEFGLSWIFLAAILKGVQCADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSGGEYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNGHSNNTVHDRTPYRTLLMNELGVPFHLGTRQVCMAWSSSSCHDGKAWLHVCITGNDNNATASFIYNGRLVDSIGSWSKNILRTQESECVCINGTCTVVMTDGSASGKADTKILFVEEGKIVHISTLSGSAQHVEECSCYPRFPGVRCVCRDNWKGSNRPIVDINVKNYSIVSSYVCSGLVGDTPRKSDSVSSSYCLDPNNEKGGHGVKGWAFDDGNDVWMGRTINETLRLGYETFKVIEGWSKANSKLQTNRQVIVEKGDRSGYSGIFSVEGKSCINRCFYVELIRGRKEETKVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI

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 \(c\).

\(|P_{f(8CQN_1)}(2) \setminus P_{f(3SUR_1)}(2)|=35\), \(|P_{f(3SUR_1)}(2) \setminus P_{f(8CQN_1)}(2)|=131\). 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 1:11110000000001001000100011001000000000100011000000110110111100010001011010110000000000011100000001011100100011000010011001011000011101010011101000000110010000001001001100010100010011011011000100111110010001000110010000000011010001100100110010011000101110000100110010011001000
Pair \(Z_2\) Length of longest common subsequence
8CQN_1,3SUR_1 166 4
8CQN_1,8GAT_1 186 4
3SUR_1,8GAT_1 160 8

Newick tree

 
[
	8CQN_1:90.69,
	[
		3SUR_1:80,8GAT_1:80
	]:10.69
]

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 \((0.85)(0.8)(\frac{800 }{\log_{20} 800}-\frac{275}{\log_{20}275})=144.\)
Status Protein1 Protein2 d d1/2
Query variables 8CQN_1 3SUR_1 182 136
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]