CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4ZOU_1 7OSZ_1 1LJK_1 Letter Amino acid
9 42 12 A Alanine
4 15 14 N Asparagine
1 38 6 K Lycine
1 12 2 M Methionine
12 34 6 V Valine
0 12 6 W Tryptophan
5 16 3 Y Tyrosine
2 13 8 C Cysteine
4 22 3 Q Glutamine
5 10 1 H Histidine
6 22 3 F Phenylalanine
7 29 7 T Threonine
7 46 2 E Glutamic acid
1 32 6 I Isoleucine
21 38 8 L Leucine
4 26 2 P Proline
5 25 11 R Arginine
6 24 7 D Aspartic acid
9 33 12 G Glycine
10 23 10 S Serine 

4ZOU_1|Chain A|Structure-specific endonuclease subunit SLX4|Homo sapiens (9606)
>7OSZ_1|Chains A, B|Bifunctional glutamate/proline--tRNA ligase|Homo sapiens (9606)
>1LJK_1|Chains A, B|Lysozyme C|Gallus gallus (9031)
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 \(w=f(c)\)
4ZOU , Knot 57 119 0.76 38 87 112 
RTLLSLGLLVADFGAMVNNPHLSDVQFQTDSGEVLYAHKFVLYARCPLLIQYVNNEGFSAVEDGVLTQRVLLGDVSTEAARTFLHYLYTADTGLPPGLSSELSSLAHRFGVSELVHLCE
7OSZ , Knot 213 512 0.86 40 269 495 
GAGEGQGPKKQTRLGLEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAIWEAIKDFFDAEIKKLGVENCYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAEPIAIRPTSETVMYPAYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRTREFLWQEGHSAFATMEEAAEEVLQILDLYAQVYEELLAIPVVKGRKTEKEKFAGGDYTTTIEAFISASGRAIQGGTSHHLGQNFSKMFEIVFEDPKIPGEKQFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCGITNALSEEDKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLEVGPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASEDLKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTARDQDLEPGAPSMGAKSLCIPFKPLCELQPGAKCVCGKNPAKYYTLFGRSY
1LJK , Knot 66 129 0.82 40 104 127 
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

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 \(c\).

\(|P_{f(4ZOU_1)}(2) \setminus P_{f(7OSZ_1)}(2)|=23\), \(|P_{f(7OSZ_1)}(2) \setminus P_{f(4ZOU_1)}(2)|=205\). 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 1:00110111111011111001010010100001011010011101001111001000110110011100011110100011001100100100111111000100110011100110100
Pair \(Z_2\) Length of longest common subsequence
4ZOU_1,7OSZ_1 228 4
4ZOU_1,1LJK_1 133 3
7OSZ_1,1LJK_1 233 3

Newick tree

 
[
	7OSZ_1:12.42,
	[
		4ZOU_1:66.5,1LJK_1:66.5
	]:60.92
]

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 \((0.85)(0.8)(\frac{631 }{\log_{20} 631}-\frac{119}{\log_{20}119})=148.\)
Status Protein1 Protein2 d d1/2
Query variables 4ZOU_1 7OSZ_1 196 119
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]