CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8SMZ_1 3WZJ_1 2QDE_1 Letter Amino acid
18 12 45 A Alanine
1 16 13 N Asparagine
7 17 22 E Glutamic acid
12 26 49 L Leucine
13 30 21 K Lycine
5 24 12 S Serine
3 16 7 Y Tyrosine
3 15 13 H Histidine
7 31 27 I Isoleucine
4 5 9 F Phenylalanine
18 8 21 R Arginine
4 19 29 D Aspartic acid
2 5 4 C Cysteine
8 20 11 Q Glutamine
9 17 37 G Glycine
0 4 5 W Tryptophan
6 19 26 V Valine
3 11 9 M Methionine
7 15 19 P Proline
10 11 18 T Threonine 

8SMZ_1|Chains A, E|Histone H3.1|Homo sapiens (9606)
>3WZJ_1|Chain A|Dual specificity protein kinase TTK|Homo sapiens (9606)
>2QDE_1|Chains A, B, C, D, E, F, G, H|Mandelate racemase/muconate lactonizing enzyme family protein|Azoarcus sp. (76114)
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 \(w=f(c)\)
8SMZ , Knot 68 140 0.80 38 107 132 
GPGHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
3WZJ , Knot 144 321 0.86 40 202 306 
MECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEEMKYVLGQLVGLNLVPRGSAAGHHHHHH
2QDE , Knot 163 397 0.82 40 213 371 
MSLKITKVEVIPISTPMKRAQLMRGATLARIDGVLLKLHSDEGLVGIADAGDTSSWYRGETQDSITSMICDFFAPKVLLGEDPTKIEKIVGRMDILTRDNNQAKATVDFALHDLVGKRFGVPVYQLLGGKTIERIPLGLVLGAGEPEAVAEEALAVLREGFHFVKLKAGGPLKADIAMVAEVRRAVGDDVDLFIDINGAWTYDQALTTIRALEKYNLSKIEQPLPAWDLDGMARLRGKVATPIYADESAQELHDLLAIINKGAADGLMIKTQKAGGLLKAQRWLTLARLANLPVICGCMVGSGLEASPAAHLLAANDWIAQFPQENAGPLHIHDCLNSRDIDNDIALNVPRFEGGYLYPNDGPGLGIELNEDLVRRLVTPGKAARVVTAEGHHHHHH

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 \(c\).

\(|P_{f(8SMZ_1)}(2) \setminus P_{f(3WZJ_1)}(2)|=43\), \(|P_{f(3WZJ_1)}(2) \setminus P_{f(8SMZ_1)}(2)|=138\). 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 1:11101100000100001101100011001100011101110010000110111001000000001110011100110011001000101000111110010010111110000101101001011100101100101001
Pair \(Z_2\) Length of longest common subsequence
8SMZ_1,3WZJ_1 181 4
8SMZ_1,2QDE_1 176 4
3WZJ_1,2QDE_1 169 7

Newick tree

 
[
	8SMZ_1:90.78,
	[
		2QDE_1:84.5,3WZJ_1:84.5
	]:6.28
]

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 \((0.85)(0.8)(\frac{461 }{\log_{20} 461}-\frac{140}{\log_{20}140})=95.4\)
Status Protein1 Protein2 d d1/2
Query variables 8SMZ_1 3WZJ_1 120 84.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]