CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8ICS_1 6CFG_1 2CQR_1 Letter Amino acid
0 10 0 H Histidine
0 24 2 I Isoleucine
0 25 7 L Leucine
4 15 5 A Alanine
0 19 5 E Glutamic acid
1 19 6 G Glycine
0 12 5 Q Glutamine
0 10 0 F Phenylalanine
2 19 1 T Threonine
0 13 2 Y Tyrosine
0 15 6 R Arginine
0 15 3 D Aspartic acid
1 9 3 C Cysteine
0 19 4 P Proline
0 26 13 S Serine
0 6 2 W Tryptophan
0 18 2 V Valine
0 29 1 N Asparagine
0 25 6 K Lycine
0 6 0 M Methionine 

8ICS_1|Chain A[auth T]|DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3')|
>6CFG_1|Chain A|Hemagglutinin|Influenza A virus (A/Viet Nam/1203/2004(H5N1)) (284218)
>2CQR_1|Chain A|DnaJ homolog subfamily C member 1|Homo sapiens (9606)
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 \(w=f(c)\)
8ICS , Knot 6 8 0.52 8 7 6 
CATTAGAA
6CFG , Knot 147 334 0.85 40 214 323 
ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSPQRERRRKKR
2CQR , Knot 36 73 0.70 34 53 64 
GSSGSSGSLRKERARSAEEPWTQNQQKLLELALQQYPRGSSDCWDKIARCVPSKSKEDCIARYKLLVSGPSSG

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 \(c\).

\(|P_{f(8ICS_1)}(2) \setminus P_{f(6CFG_1)}(2)|=2\), \(|P_{f(6CFG_1)}(2) \setminus P_{f(8ICS_1)}(2)|=209\). 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 1:01001111
Pair \(Z_2\) Length of longest common subsequence
8ICS_1,6CFG_1 211 2
8ICS_1,2CQR_1 60 1
6CFG_1,2CQR_1 205 3

Newick tree

 
[
	6CFG_1:11.84,
	[
		8ICS_1:30,2CQR_1:30
	]:88.84
]

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 \((0.85)(0.8)(\frac{342 }{\log_{20} 342}-\frac{8}{\log_{20}8})=111.\)
Status Protein1 Protein2 d d1/2
Query variables 8ICS_1 6CFG_1 143 73
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: