CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4COW_1 3UHV_1 8FSR_1 Letter Amino acid
6 2 14 M Methionine
21 4 33 Y Tyrosine
11 15 33 K Lycine
16 3 37 P Proline
20 6 28 T Threonine
3 2 20 W Tryptophan
6 1 0 C Cysteine
5 3 26 E Glutamic acid
20 10 27 G Glycine
24 13 41 D Aspartic acid
3 6 25 Q Glutamine
11 2 4 H Histidine
24 12 49 L Leucine
10 14 31 V Valine
15 18 54 A Alanine
7 4 37 R Arginine
19 9 35 N Asparagine
5 9 24 I Isoleucine
15 6 29 F Phenylalanine
26 7 38 S Serine 

4COW_1|Chain A|EPITHELIAL ADHESIN 6|CANDIDA GLABRATA (284593)
>3UHV_1|Chains A, B|Globin-1|Scapharca inaequivalvis (2784303)
>8FSR_1|Chain A|YejA|Escherichia coli (562)
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 \(w=f(c)\)
4COW , Knot 116 267 0.81 40 162 252 
MGSSHHHHHHSSGLVPRGSHMKDDYSSSLSNNNLGWTDPTEFPLGCSPNVTTPKNGLSMELYSYDYLKSGSNPCWDAAYLDPNYPRTGYKSHRLLAKVENVAGNINFYYHAPMGCTSLFDTLPQAYNYRTPLTMTNFTMLLYGYFKPKVTGYHTFTISADDLLFVNFGAGNAFDCCKRESSADDFGNYQAYAVWGSQTAKDDLTVHLDAGLYYPIRIFFNNRDNDGALSLTLKTESDPNPVIDFSDYFYSFDDTKDGCPGLVSYDTS
3UHV , Knot 73 146 0.83 40 112 144 
PSVYDAAAQLTADVKKDLRDSWKVIGSDKKGNGVALVTTLFADNQETIGYFKRLGDVSQGMANDKLRGHSITIMYALQNFIDQLDNPDDLVCVVEKFAVNHITRKISAAEFGKINGPIKKVLASKNFGDKYANAWAKLVAVVQAAL
8FSR , Knot 235 585 0.85 38 268 559 
QAIKESYAFAVLGEPRYAFNFNHFDYVNPAAPKGGQITLSALGTFDNFNRYALRGNPGARTEQLYDTLFTTSDDEPGSYYPLIAESARYADDYSWVEVAINPRARFHDGSPITARDVEFTFQKFMTEGVPQFRLVYKGTTVKAIAPLTVRIELAKPGKEDMLSLFSLPVFPEKYWKDHKLSDPLATPPLASGPYRVTSWKMGQNIVYSRVKDYWAANLPVNRGRWNFDTIRYDYYLDDNVAFEAFKAGAFDLRMENDAKNWATRYTGKNFDKKYIIKDEQKNESAQDTRWLAFNIQRPVFSDRRVREAITLAFDFEWMNKALFYNAWSRTNSYFQNTEYAARNYPDAAELVLLAPMKKDLPSEVFTQIYQPPVSKGDGYDRDNLLKADKLLNEAGWVLKGQQRVNATTGQPLSFELLLPASSNSQWVLPFQHSLQRLGINMDIRKVDNSQITNRMRSRDYDMMPRVWRAMPWPSSDLQISWSSEYINSTYNAPGVQSPVIDSLINQIIAAQGNKEKLLPLGRALDRVLTWNYYMLPMWYMAEDRLAWWDKFSQPAVRPVYSLGIDTWWYDVNKAAKLPSASKQGE

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 \(c\).

\(|P_{f(4COW_1)}(2) \setminus P_{f(3UHV_1)}(2)|=107\), \(|P_{f(3UHV_1)}(2) \setminus P_{f(4COW_1)}(2)|=57\). 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 1:110000000000111101001000000010000111001001111001010010011010100000100100101011010100100100000111010011101010001111000110011010000011010010111010101010100010101001111011110110000000010011000101111000100010101011100110111000000111010100000101110100010010000010111100000
Pair \(Z_2\) Length of longest common subsequence
4COW_1,3UHV_1 164 4
4COW_1,8FSR_1 184 4
3UHV_1,8FSR_1 194 4

Newick tree

 
[
	8FSR_1:98.35,
	[
		4COW_1:82,3UHV_1:82
	]:16.35
]

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 \((0.85)(0.8)(\frac{413 }{\log_{20} 413}-\frac{146}{\log_{20}146})=79.9\)
Status Protein1 Protein2 d d1/2
Query variables 4COW_1 3UHV_1 99 77
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]