CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2EVJ_1 3SYK_1 7BWI_1 Letter Amino acid
2 22 8 G Glycine
0 15 3 I Isoleucine
0 11 5 Y Tyrosine
0 14 1 V Valine
0 10 2 F Phenylalanine
1 17 6 T Threonine
0 11 1 N Asparagine
0 20 1 D Aspartic acid
0 9 0 Q Glutamine
0 9 0 H Histidine
0 8 0 M Methionine
0 11 2 P Proline
0 0 1 W Tryptophan
6 36 0 A Alanine
0 31 1 R Arginine
5 0 6 C Cysteine
0 26 0 E Glutamic acid
0 35 1 L Leucine
0 11 2 K Lycine
0 13 2 S Serine 

2EVJ_1|Chain A[auth B]|5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*CP*AP*C)-3'|
>3SYK_1|Chains A, B|Protein CbbX|Rhodobacter sphaeroides (1063)
>7BWI_1|Chain A|Kappa-actitoxin-Ael2a|Anthopleura elegantissima (6110)
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 \(w=f(c)\)
2EVJ , Knot 7 14 0.44 8 7 9 
TGCGACACAAACAC
3SYK , Knot 130 309 0.80 36 182 292 
MTDAATAPTSIDLRAEYEGSGAKEVLEELDRELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRAMGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNALDRARLRQANRLFTASSGPLDARALSTIAEEDIRASRVFKGGLDSERRAAEALAR
7BWI , Knot 24 42 0.71 30 34 40 
GTTCYCGKTIGIYWFGTKTCPSNRGYTGSCGYFLGICCYPVD

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 \(c\).

\(|P_{f(2EVJ_1)}(2) \setminus P_{f(3SYK_1)}(2)|=4\), \(|P_{f(3SYK_1)}(2) \setminus P_{f(2EVJ_1)}(2)|=179\). 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 1:01011010111010
Pair \(Z_2\) Length of longest common subsequence
2EVJ_1,3SYK_1 183 2
2EVJ_1,7BWI_1 37 2
3SYK_1,7BWI_1 188 3

Newick tree

 
[
	3SYK_1:10.57,
	[
		2EVJ_1:18.5,7BWI_1:18.5
	]:88.07
]

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 \((0.85)(0.8)(\frac{323 }{\log_{20} 323}-\frac{14}{\log_{20}14})=103.\)
Status Protein1 Protein2 d d1/2
Query variables 2EVJ_1 3SYK_1 126 65
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: