CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6OVT_1 1UCV_1 7BHO_1 Letter Amino acid
79 5 26 A Alanine
11 1 0 N Asparagine
45 4 0 D Aspartic acid
55 8 0 L Leucine
18 1 0 F Phenylalanine
30 1 0 P Proline
35 6 0 R Arginine
8 5 0 Q Glutamine
69 14 7 G Glycine
18 2 0 H Histidine
29 4 0 I Isoleucine
19 5 0 M Methionine
30 5 10 T Threonine
10 2 0 Y Tyrosine
8 0 14 C Cysteine
16 2 0 K Lycine
51 3 0 V Valine
29 0 0 E Glutamic acid
39 12 0 S Serine
1 1 0 W Tryptophan 

6OVT_1|Chains A, B, C, D|Dihydroxy-acid dehydratase|Mycobacterium tuberculosis (1773)
>1UCV_1|Chain A|EPHRIN TYPE-A RECEPTOR 8|Homo sapiens (9606)
>7BHO_1|Chain A[auth A1]|DNA|Escherichia virus M13 (1977402)
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 \(w=f(c)\)
6OVT , Knot 226 600 0.80 40 227 527 
MSYYHHHHHHDYDIPTTENLYFQGAMPQTTDEAASVSTVADIKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAVKEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLAGCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLMSRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSGQAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSRIGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAITPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAALDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTTGLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTTGVLSKYVKLVSSAAVGAVCG
1UCV , Knot 41 81 0.74 36 63 76 
GSSGSSGLTVGDWLDSIRMGRYRDHFAAGGYSSLGMVLRMNAQDVRALGITLMGHQKKILGSIQTMRAQLTSTQGSGPSSG
7BHO , Knot 19 57 0.44 8 15 33 
TAAGTACAACCACAGCATTCCAGAACACGTCAACAAATAAGGAACAAAACTCGTATT

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 \(c\).

\(|P_{f(6OVT_1)}(2) \setminus P_{f(1UCV_1)}(2)|=182\), \(|P_{f(1UCV_1)}(2) \setminus P_{f(6OVT_1)}(2)|=18\). 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 1:100000000000011000010101111000001101001101010000100110011101110111100001101011110010010100101001101100111011101101101010011011001101011000111001011101001010111110000111111111010111111011011110101001000010110110111100011100101011001101101101110010011011011110111011111000000111000101110110011010011000110011111111110001110111110010111010010011011101101011100110010011111111011101111010010101001100111101101010110111011010111011010111011110011100011010101101001110110010101101111000110111110011110111011111001111001010110011011011101101111111001001010111011011101101100000101111000011100010110011111101
Pair \(Z_2\) Length of longest common subsequence
6OVT_1,1UCV_1 200 4
6OVT_1,7BHO_1 220 3
1UCV_1,7BHO_1 72 4

Newick tree

 
[
	6OVT_1:11.58,
	[
		1UCV_1:36,7BHO_1:36
	]:83.58
]

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 \((0.85)(0.8)(\frac{681 }{\log_{20} 681}-\frac{81}{\log_{20}81})=175.\)
Status Protein1 Protein2 d d1/2
Query variables 6OVT_1 1UCV_1 208 117
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]