CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6ANN_1 1YFG_1 2BYP_1 Letter Amino acid
1 16 11 A Alanine
0 24 4 C Cysteine
0 0 11 Q Glutamine
0 0 3 H Histidine
0 0 9 I Isoleucine
0 0 11 Y Tyrosine
0 0 22 D Aspartic acid
0 0 9 E Glutamic acid
0 0 5 M Methionine
0 0 17 V Valine
0 0 10 R Arginine
0 25 8 G Glycine
0 0 8 F Phenylalanine
0 0 7 N Asparagine
1 0 16 L Leucine
0 0 9 K Lycine
0 0 12 P Proline
0 0 21 S Serine
0 0 17 T Threonine
0 0 4 W Tryptophan 

6ANN_1|Chains A, B, C, D, E|cyclic DLE-ZAE-BE2-DAL|synthetic construct (32630)
>1YFG_1|Chain A|YEAST INITIATOR TRNA|Saccharomyces cerevisiae (4932)
>2BYP_1|Chains A, B, C, D, E|SOLUBLE ACETYLCHOLINE RECEPTOR|APLYSIA CALIFORNICA (6500)
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 \(w=f(c)\)
6ANN , Knot 3 4 0.34 6 3 2 
LXXA
1YFG , Knot 23 75 0.44 8 15 43 
AGCGCCGUGGCGCAGUGGAAGCGCGCAGGGCUCAUAACCCUGAUGUCCUCGGAUCGAAACCGAGCGGCGCUACCA
2BYP , Knot 100 214 0.83 40 156 208 
DDDDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR

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 \(c\).

\(|P_{f(6ANN_1)}(2) \setminus P_{f(1YFG_1)}(2)|=3\), \(|P_{f(1YFG_1)}(2) \setminus P_{f(6ANN_1)}(2)|=15\). 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 1:1001
Pair \(Z_2\) Length of longest common subsequence
6ANN_1,1YFG_1 18 1
6ANN_1,2BYP_1 159 1
1YFG_1,2BYP_1 163 2

Newick tree

 
[
	2BYP_1:92.81,
	[
		6ANN_1:9,1YFG_1:9
	]:83.81
]

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 \((0.85)(0.8)(\frac{79 }{\log_{20} 79}-\frac{4}{\log_{20}4})=30.9\)
Status Protein1 Protein2 d d1/2
Query variables 6ANN_1 1YFG_1 22 12.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: