CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7CVZ_1 3ZEA_1 3IVB_1 Letter Amino acid
27 19 3 P Proline
34 14 4 T Threonine
4 5 3 W Tryptophan
21 6 4 Y Tyrosine
13 6 7 R Arginine
9 6 3 M Methionine
15 13 11 F Phenylalanine
17 12 4 C Cysteine
21 19 11 E Glutamic acid
22 17 16 K Lycine
15 4 3 Q Glutamine
27 33 11 G Glycine
12 8 0 H Histidine
20 14 4 I Isoleucine
23 18 15 L Leucine
46 24 6 A Alanine
15 11 6 N Asparagine
16 15 9 D Aspartic acid
35 11 15 S Serine
47 28 10 V Valine 

7CVZ_1|Chains A, F[auth D], H[auth G], N[auth J]|E1 glycoprotein|Chikungunya virus (37124)
>3ZEA_1|Chain A|PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT|DESULFOVIBRIO VULGARIS (881)
>3IVB_1|Chain A|Speckle-type POZ protein|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 \(w=f(c)\)
7CVZ , Knot 180 439 0.83 40 242 414 
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKRTTVYYPASHTTLGVQDISATAMSWVQKITGGVGLVVAVAALILIVVLCVSFSRH
3ZEA , Knot 127 283 0.84 40 175 277 
GTLTGERPPVFWLQGQGCTGCSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRNIHENCPYLDKYDEGVMSATFTDKVGCRYDLGCKGPMTMADCFERKWNGGVNWCVQNAVCIGCVEPDFPDGKSPFYQA
3IVB , Knot 70 145 0.80 38 106 139 
GSGGSGKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQD

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 \(c\).

\(|P_{f(7CVZ_1)}(2) \setminus P_{f(3ZEA_1)}(2)|=114\), \(|P_{f(3ZEA_1)}(2) \setminus P_{f(7CVZ_1)}(2)|=47\). 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 1:0001011100111100011001100111101011010101010100100000011101010001010000001100000110110111111100100100001001010000000001101001001010101011001001010101010011010010111111001101100011100101001001111110110110100001000010100011100111101011000110110011000110100011110011001101100111011101011011100110110100100011100000011111110011000100110010011010010101010001010100111010101010000100110001100001001100001110010101101100101111111111111111110101000
Pair \(Z_2\) Length of longest common subsequence
7CVZ_1,3ZEA_1 161 4
7CVZ_1,3IVB_1 194 4
3ZEA_1,3IVB_1 179 3

Newick tree

 
[
	3IVB_1:97.22,
	[
		7CVZ_1:80.5,3ZEA_1:80.5
	]:16.72
]

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 \((0.85)(0.8)(\frac{722 }{\log_{20} 722}-\frac{283}{\log_{20}283})=121.\)
Status Protein1 Protein2 d d1/2
Query variables 7CVZ_1 3ZEA_1 154 125.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]