CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6NYN_1 9HJO_1 1AEC_1 Letter Amino acid
25 8 14 Y Tyrosine
61 8 16 A Alanine
99 13 14 N Asparagine
8 7 1 H Histidine
33 7 5 F Phenylalanine
71 11 19 T Threonine
57 22 8 L Leucine
57 12 6 K Lycine
53 21 18 I Isoleucine
40 9 12 D Aspartic acid
2 6 7 C Cysteine
26 14 9 Q Glutamine
27 17 13 E Glutamic acid
86 11 28 G Glycine
53 18 17 V Valine
22 14 5 R Arginine
10 8 2 M Methionine
21 4 7 P Proline
59 24 11 S Serine
11 0 6 W Tryptophan 

6NYN_1|Chains A, B, C, D, E, F, G, H, I, J, K, L|Vacuolating cytotoxin autotransporter|Helicobacter pylori (210)
>9HJO_1|Chains A, C|Fanconi anemia group M protein|Homo sapiens (9606)
>1AEC_1|Chain A|ACTINIDIN|Actinidia chinensis (3625)
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 \(w=f(c)\)
6NYN , Knot 302 821 0.82 40 265 723 
AFFTTVIIPAIVGGIATGTAVGTVSGLLGWGLKQAEEANKTPDKPDKVWRIQAGKGFNEFPNKEYDLYKSLLSSKIDGGWDWGNAATHYWIKGGQWNKLEVDMKDAVGTYKLSGLRNFTGGDLDVNMQKATLRLGQFNGNSFTSYKDSADRTTRVDFNAKNILIDNFLEINNRVGSGAGRKASSTVLTLQASEGITSSKNAEISLYDGATLNLASNSVKLNGNVWMGRLQYVGAYLAPSYSTINTSKVTGEVNFNHLTVGDHNAAQAGIIASNKTHIGTLDLWQSAGLNIIAPPEGGYKDKPNNTPSQSGAKNDKQESSQNNSNTQVINPPNSTQKTEVQPTQVIDGPFAGGKDTVVNIDRINTKADGTIKVGGFKASLTTNAAHLNIGKGGVNLSNQASGRTLLVENLTGNITVDGPLRVNNQVGGYALAGSSANFEFKAGVDTKNGTATFNNDISLGRFVNLKVDAHTANFKGIDTGNGGFNTLDFSGVTNKVNINKLITASTNVAVKNFNINELIVKTNGVSVGEYTHFSEDIGSQSRINTVRLETGTRSIFSGGVKFKSGEKLVIDEFYYSPWNYFDARNIKNVEITRKFASSTPENPWGTSKLMFNNLTLGQNAVMDYSQFSNLTIQGDFINNQGTINYLVRGGKVATLNVGNAAAMMFNNDIDSATGFYKPLIKINSAQDLIKNTEHVLLKAKIIGYGNVSTGTNGISNVNLEEQFKERLALYNNNNRMDTCVVRNTDDIKACGMAIGNQSMVNNPDNYKYLIGKAWKNIGISKTANGSKISVYYLGNSTPTENGGNTTNLPTNTTNNARFASYA
9HJO , Knot 108 234 0.84 38 160 230 
GKGTCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREKTGDTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKNVGIHVPTVVNSNKSEALQFYLSIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQVTHQKAEEIYRYIHYVFDIQMLPNDLNQDRLKSDI
1AEC , Knot 99 218 0.81 40 142 208 
LPSYVDWRSAGAVVDIKSQGECGGCWAFSAIATVEGINKIVTGVLISLSEQELIDCGRTQNTRGCNGGYITDGFQFIINNGGINTEENYPYTAQDGECNVDLQNEKYVTIDTYENVPYNNEWALQTAVTYQPVSVALDAAGDAFKQYSSGIFTGPCGTAIDHAVTIVGYGTEGGIDYWIVKNSWDTTWGEEGYMRILRNVGGAGTCGIATMPSYPVKY

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 \(c\).

\(|P_{f(6NYN_1)}(2) \setminus P_{f(9HJO_1)}(2)|=142\), \(|P_{f(9HJO_1)}(2) \setminus P_{f(6NYN_1)}(2)|=37\). 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 1:11100111111111110101110101111111001001000100100110101101100110000010001100010111011011000110110100101010011100010110010110101010010101101010010000001000001010100111001101000110111001000110101001100000101010011010110001010101111010011101110000100001010101001011000110111110000011010110011101111101100001000100011000000000000000110110000000101001101111110001101001000101010111101010001101011011101000101001110010101010111010001110111100101010111000010101000101101101010100101011001011100101011000101001101000111001010011100011011000010001100001001010010001101110100100111001000110010100100101000110001001110001110010110011100001001010101100010100110110110101101111110001001011001110100100110000011101011101010010011001010001000111000000100011000001010111110001100100000111011001110001010010100110001000110000110000001011001
Pair \(Z_2\) Length of longest common subsequence
6NYN_1,9HJO_1 179 4
6NYN_1,1AEC_1 171 4
9HJO_1,1AEC_1 178 3

Newick tree

 
[
	9HJO_1:90.46,
	[
		6NYN_1:85.5,1AEC_1:85.5
	]:4.96
]

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 \((0.85)(0.8)(\frac{1055 }{\log_{20} 1055}-\frac{234}{\log_{20}234})=221.\)
Status Protein1 Protein2 d d1/2
Query variables 6NYN_1 9HJO_1 275 176.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]