CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2DKN_1 5SKY_1 7QWE_1 Letter Amino acid
11 31 0 T Threonine
26 43 0 V Valine
45 34 8 A Alanine
16 22 0 R Arginine
11 34 0 D Aspartic acid
4 23 0 C Cysteine
11 25 4 I Isoleucine
6 30 0 F Phenylalanine
32 29 2 G Glycine
4 30 5 K Lycine
10 26 0 P Proline
1 10 0 W Tryptophan
4 25 1 Y Tyrosine
4 27 0 N Asparagine
9 16 2 Q Glutamine
14 15 4 E Glutamic acid
3 20 0 H Histidine
5 14 0 M Methionine
25 40 4 L Leucine
14 29 0 S Serine 

2DKN_1|Chains A, B|3-alpha-hydroxysteroid dehydrogenase|Pseudomonas sp. (402890)
>5SKY_1|Chain A[auth D]|Proofreading exoribonuclease nsp14|Severe acute respiratory syndrome coronavirus 2 (2697049)
>7QWE_1|Chains A, B, C, D, E, F, G, H, I, J|CC-Type2-(Ug)4|synthetic construct (32630)
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 \(w=f(c)\)
2DKN , Knot 110 255 0.79 40 140 236 
MSVIAITGSASGIGAALKELLARAGHTVIGIDRGQADIEADLSTPGGRETAVAAVLDRCGGVLDGLVCCAGVGVTAANSGLVVAVNYFGVSALLDGLAEALSRGQQPAAVIVGSIAATQPGAAELPMVEAMLAGDEARAIELAEQQGQTHLAYAGSKYAVTCLARRNVVDWAGRGVRLNVVAPGAVETPLLQASKADPRYGESTRRFVAPLGRGSEPREVAEAIAFLLGPQASFIHGSVLFVDGGMDALMRAKTF
5SKY , Knot 217 523 0.86 40 267 499 
SMLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ
7QWE , Knot 13 32 0.46 18 15 17 
XGEIAQALKEIAKALKEIAYALKEIAQALKGX

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 \(c\).

\(|P_{f(2DKN_1)}(2) \setminus P_{f(5SKY_1)}(2)|=35\), \(|P_{f(5SKY_1)}(2) \setminus P_{f(2DKN_1)}(2)|=162\). 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 1:101111010101111110011101100111100101010101001110001111110001111011100111110110011111100111011101110110010011111110111001111011110111110010110110001000110110001100110001101110110101111111001110100101001000001111110100100110111111110101101011110111011101001
Pair \(Z_2\) Length of longest common subsequence
2DKN_1,5SKY_1 197 3
2DKN_1,7QWE_1 135 4
5SKY_1,7QWE_1 264 2

Newick tree

 
[
	5SKY_1:12.70,
	[
		2DKN_1:67.5,7QWE_1:67.5
	]:61.20
]

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 \((0.85)(0.8)(\frac{778 }{\log_{20} 778}-\frac{255}{\log_{20}255})=144.\)
Status Protein1 Protein2 d d1/2
Query variables 2DKN_1 5SKY_1 187 135.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]