CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3NQW_1 5DQB_1 7RPE_1 Letter Amino acid
10 17 15 T Threonine
7 11 12 S Serine
4 2 0 C Cysteine
14 22 24 K Lycine
3 5 10 M Methionine
5 10 8 P Proline
2 2 6 W Tryptophan
13 7 7 R Arginine
10 9 11 Q Glutamine
14 16 21 E Glutamic acid
6 25 20 G Glycine
3 14 4 H Histidine
6 12 8 F Phenylalanine
4 8 7 Y Tyrosine
15 16 15 V Valine
14 10 16 A Alanine
15 18 6 D Aspartic acid
6 13 16 I Isoleucine
20 20 22 L Leucine
8 13 17 N Asparagine 

3NQW_1|Chains A, B|CG11900|Drosophila melanogaster (7227)
>5DQB_1|Chain A|WasCFP_pH2|Aequorea coerulescens (210840)
>7RPE_1|Chain A|Beta-lactamase|Acinetobacter baumannii (470)
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 \(w=f(c)\)
3NQW , Knot 87 179 0.84 40 133 173 
MATYPSAKFMECLQYAAFKHRQQRRKDPQETPYVNHVINVSTILSVEACITDEGVLMAALLHDVVEDTDASFEDVEKLFGPDVCGLVREVTDDKSLEKQERKRLQIENAAKSSCRAKLIKLADKLDNLRDLQVNTPTGWTQERRDQYFVWAKKVVDNLRGTNANLELKLDEIFRQRGLL
5DQB , Knot 110 250 0.81 40 162 232 
MRGSHHHHHHGSVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLKTTLTWGVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNAISGNVNITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKQSKDPNEKRDHMVLLEFVTAAGITLGMDELYK
7RPE , Knot 112 245 0.83 38 161 230 
MHISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII

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 \(c\).

\(|P_{f(3NQW_1)}(2) \setminus P_{f(5DQB_1)}(2)|=63\), \(|P_{f(5DQB_1)}(2) \setminus P_{f(3NQW_1)}(2)|=92\). 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 1:11001010110010011100000000010001010011010011010101000111111110011000010100100111101011100100000100000001010011000001011011001001001010010110000000011110011001010010101010011000111
Pair \(Z_2\) Length of longest common subsequence
3NQW_1,5DQB_1 155 3
3NQW_1,7RPE_1 152 4
5DQB_1,7RPE_1 143 3

Newick tree

 
[
	3NQW_1:78.42,
	[
		7RPE_1:71.5,5DQB_1:71.5
	]:6.92
]

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 \((0.85)(0.8)(\frac{429 }{\log_{20} 429}-\frac{179}{\log_{20}179})=73.8\)
Status Protein1 Protein2 d d1/2
Query variables 3NQW_1 5DQB_1 94 80.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]