CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3ASX_1 8DZU_1 5BKM_1 Letter Amino acid
24 9 51 A Alanine
22 7 17 E Glutamic acid
24 5 19 I Isoleucine
4 1 4 W Tryptophan
21 9 40 V Valine
23 5 30 S Serine
19 2 31 R Arginine
20 5 13 Q Glutamine
7 3 16 H Histidine
31 7 36 L Leucine
18 11 17 K Lycine
12 4 8 M Methionine
16 8 14 F Phenylalanine
14 5 16 Y Tyrosine
22 12 44 D Aspartic acid
11 4 38 P Proline
15 6 18 N Asparagine
7 1 10 C Cysteine
13 13 45 G Glycine
17 7 25 T Threonine 

3ASX_1|Chain A|Squalene synthase|Homo sapiens (9606)
>8DZU_1|Chain A|Photoactive yellow protein|Halorhodospira halophila (1053)
>5BKM_1|Chain A|Carboxylesterase A|Mycobacterium tuberculosis (83332)
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 \(w=f(c)\)
3ASX , Knot 149 340 0.85 40 214 327 
MDQDSLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQN
8DZU , Knot 66 125 0.85 42 102 120 
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTXDYQHTPTKVKVHMKKALSGDSYWVFVKRV
5BKM , Knot 198 492 0.83 40 248 447 
MGSSHHHHHHSSGLVPRGSHMVEWTPCRSSNPQVKIPGGALCGKLAVPVDYDRPDGDVAALALIRFPATGDKIGSLVINPGGPGESGIEAALGVFQTLPKRVHERFDLVGFDPRGVASSRPAIWCNSDADNDRLRAEPQVDYSREGVAHIENETKQFVGRCVDKMGKNFLAHVGTVNVAKDLDAIRAALGDDKLTYLGYSYGTRIGSAYAEEFPQRVRAMILDGAVDPNADPIEAELRQAKGFQDAFNNYAADCAKNAGCPLGADPAKAVEVYHSLVDPLVDPDNPRISRPARTKDPRGLSYSDAIVGTIMALYSPNLWQHLTDGLSELVDNRGDTLLALADMYMRRDSHGRYNNSGDARVAINCVDQPPVTDRDKVIDEDRRAREIAPFMSYGKFTGDAPLGTCAFWPVPPTSQPHAVSAPGLVPTVVVSTTHDPATPYKAGVDLANQLRGSLLTFDGTQHTVVFQGDSCIDEYVTAYLIGGTTPPSGAKC

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 \(c\).

\(|P_{f(3ASX_1)}(2) \setminus P_{f(8DZU_1)}(2)|=157\), \(|P_{f(8DZU_1)}(2) \setminus P_{f(3ASX_1)}(2)|=45\). 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 1:1000010001000000100000011111011010100110110111011001000101010001111001001100101011000000001100110101010011000001110100011111101100010000010000001111111110011010010011110000010011111000011000100001100111001100010011011010010111001001100110011011001001000011010111011111011100000011011101001011011101001111011100010010001100010000000110010000
Pair \(Z_2\) Length of longest common subsequence
3ASX_1,8DZU_1 202 3
3ASX_1,5BKM_1 188 4
8DZU_1,5BKM_1 208 4

Newick tree

 
[
	8DZU_1:10.19,
	[
		3ASX_1:94,5BKM_1:94
	]:11.19
]

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 \((0.85)(0.8)(\frac{465 }{\log_{20} 465}-\frac{125}{\log_{20}125})=101.\)
Status Protein1 Protein2 d d1/2
Query variables 3ASX_1 8DZU_1 132 89.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]