CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2DYM_1 1OHB_1 7VRP_1 Letter Amino acid
6 5 3 H Histidine
17 10 23 P Proline
17 12 45 T Threonine
7 2 19 Y Tyrosine
8 8 9 M Methionine
12 9 16 R Arginine
3 1 2 C Cysteine
17 27 42 G Glycine
30 18 30 I Isoleucine
28 37 44 L Leucine
19 13 10 K Lycine
9 30 33 A Alanine
18 3 15 F Phenylalanine
28 11 38 S Serine
8 2 2 W Tryptophan
15 11 22 N Asparagine
15 15 23 D Aspartic acid
9 11 16 Q Glutamine
13 13 15 E Glutamic acid
18 20 34 V Valine 

2DYM_1|Chains A, C, E, G|Autophagy protein 5|Saccharomyces cerevisiae (4932)
>1OHB_1|Chain A|ACETYLGLUTAMATE KINASE|ESCHERICHIA COLI BL21(DE3) (469008)
>7VRP_1|Chains A, B, C, D, E, F, G, H, I, J, K, L, M|Structural polyprotein|Avian infectious bursal disease virus (10995)
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 \(w=f(c)\)
2DYM , Knot 130 297 0.83 40 183 282 
GAHMNDIKQLLWNGELNVLVSIDPSFLMKGSPREIAVLRIRVPRETYLVNYMPLIWNKIKSFLSFDPLTDSEKYFWFEHNKTPIPWNYPVGVLFDCLAGKSATFTTSFENQVKDVLTFLRIHLVMGDSLPPTIIPIASSKTQAEKFWFHQWKQVCFILNGSSKAIMSLSVNEARKFWGSVITRNFQDFIEISNKISSSRPRHIPLIIQTSRTSGTFRISQPTISMTGVNPTLKDIEGDILDVKEGINGNDVMVICQGIEIPWHMLLYDLYSKLRSFDGFLYITLVPIKGGDKASSEL
1OHB , Knot 111 258 0.79 40 150 245 
MMNPLIIKLGGVLLDSEEALERLFSALVNYRESHQRPLVIVHGGGCVVDELMKGLNLPVKKKNGLRVTPADQIDIITGALAGTANKTLLAWAKKHQIAAVGLFLGDGDSVKVTQLDEELGHVGLAQPGSPKLINSLLENGYLPVVSSIGVTDEGQLMNVNADQAATALAATLGADLILLSDVSGILDGKGQRIAEMTAAKAEQLIEQGIITDGMIVKVNAALDAARTLGRPVDIASWRHAEQLPALFNGMPMGTRILA
7VRP , Knot 178 441 0.82 40 211 408 
MTNLQDQTQQIVPFIRSLLMPTTGPASIPDDTLEKHTLRSETSTYNLTVGDTGSGLIVFFPGFPGSIVGAHYTLQSNGNYKFDQMLLTAQNLPASYNYCRLVSRSLTVRSSTLPGGVYALNGTINAVTFQGSLSELTDVSYNGLMSATANINDKIGNVLVGEGVTVLSLPTSYDLGYVRLGDPIPAIGLDPKMVATCDSSDRPRVYTITAADDYQFSSQYQAGGVTITLFSANIDAITSLSIGGELVFQTSVQGLILGATIYLIGFDGTAVITRAVAADNGLTAGTDNLMPFNIVIPTSEITQPITSIKLEIVTSKSGGQAGDQMSWSASGSLAVTIHGGNYPGALRPVTLVAYERVATGSVVTVAGVSNFELIPNPELAKNLVTEYGRFDPGAMNYTKLILSERDRLGIKTVWPTREYTDFREYFMEVADLNSPLKIAGA

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 \(c\).

\(|P_{f(2DYM_1)}(2) \setminus P_{f(1OHB_1)}(2)|=92\), \(|P_{f(1OHB_1)}(2) \setminus P_{f(2DYM_1)}(2)|=59\). 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 1:110100100111010101110101011101010011110101100001100111110010011010110000001110000011110011111100111001010001000100110110101111001110111110000010011100100101110100011101010010011101100010011010001000010011111000000101010010101011010100101011010011010011110011011101110010001001011101011110110010001
Pair \(Z_2\) Length of longest common subsequence
2DYM_1,1OHB_1 151 4
2DYM_1,7VRP_1 160 4
1OHB_1,7VRP_1 153 4

Newick tree

 
[
	7VRP_1:79.17,
	[
		2DYM_1:75.5,1OHB_1:75.5
	]:3.67
]

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 \((0.85)(0.8)(\frac{555 }{\log_{20} 555}-\frac{258}{\log_{20}258})=84.2\)
Status Protein1 Protein2 d d1/2
Query variables 2DYM_1 1OHB_1 106 97
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]