CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5OXE_1 1TFA_1 6CQM_1 Letter Amino acid
6 15 6 I Isoleucine
11 24 8 L Leucine
4 13 2 P Proline
1 22 7 D Aspartic acid
0 12 0 C Cysteine
3 3 2 M Methionine
2 12 6 R Arginine
1 13 5 Q Glutamine
1 7 1 H Histidine
4 28 8 K Lycine
5 25 10 S Serine
7 23 7 V Valine
0 5 1 W Tryptophan
4 12 6 Y Tyrosine
12 30 9 A Alanine
2 12 11 N Asparagine
0 19 10 E Glutamic acid
11 24 8 G Glycine
3 12 5 F Phenylalanine
4 18 7 T Threonine 

5OXE_1|Chain A|Major virion protein|Aeropyrum pernix bacilliform virus 1 (1289471)
>1TFA_1|Chain A|PROTEIN (OVOTRANSFERRIN)|Gallus gallus (9031)
>6CQM_1|Chains A, B, C, D, E, F, G, H|Single-stranded DNA-binding protein RIM1, mitochondrial|Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (559292)
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 \(w=f(c)\)
5OXE , Knot 43 81 0.77 34 65 78 
MAPKATLVKKFKGLAVGVGALLAAPPIMGLASYAVNGISSYLSITINSTTYDFAPLAQAVMVFGGIGLVAYGLHRILGRGL
1TFA , Knot 142 329 0.83 40 209 315 
KSVIRWCTVSSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQVFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLGRSAGWNIPIGTLIHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYKTCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMR
6CQM , Knot 62 119 0.83 38 98 117 
MDFSKMSIVGRIGSEFTEHTSANNNRYLKYSIASQPRRDGQTNWYNITVFNEPQINFLTEYVRKGALVYVEADAANYVFERDDGSKGTTLSLVQKDINLLKNGKKLEDAEGQENAASSE

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 \(c\).

\(|P_{f(5OXE_1)}(2) \setminus P_{f(1TFA_1)}(2)|=19\), \(|P_{f(1TFA_1)}(2) \setminus P_{f(5OXE_1)}(2)|=163\). 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 1:111010110010111111111111111111100110110001010100000011111011111111111101100111011
Pair \(Z_2\) Length of longest common subsequence
5OXE_1,1TFA_1 182 3
5OXE_1,6CQM_1 117 3
1TFA_1,6CQM_1 171 4

Newick tree

 
[
	1TFA_1:96.19,
	[
		5OXE_1:58.5,6CQM_1:58.5
	]:37.69
]

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 \((0.85)(0.8)(\frac{410 }{\log_{20} 410}-\frac{81}{\log_{20}81})=101.\)
Status Protein1 Protein2 d d1/2
Query variables 5OXE_1 1TFA_1 127 77.5
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: