CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8YBB_1 7GSC_1 5ULW_1 Letter Amino acid
29 29 0 L Leucine
13 14 0 F Phenylalanine
18 17 0 V Valine
7 11 0 H Histidine
9 18 0 D Aspartic acid
14 30 0 E Glutamic acid
11 18 0 I Isoleucine
9 23 0 K Lycine
8 9 0 Y Tyrosine
20 13 2 A Alanine
2 11 0 N Asparagine
17 13 0 T Threonine
9 19 0 R Arginine
7 14 0 Q Glutamine
24 14 2 G Glycine
4 11 0 M Methionine
3 22 0 P Proline
20 25 0 S Serine
8 6 0 W Tryptophan
1 4 3 C Cysteine 

8YBB_1|Chains A, B, C, D, E, F|Sigma non-opioid intracellular receptor 1|Xenopus laevis (8355)
>7GSC_1|Chain A|Tyrosine-protein phosphatase non-receptor type 1|Homo sapiens (9606)
>5ULW_1|Chain A[auth P]|DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3')|unidentified (32644)
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 \(w=f(c)\)
8YBB , Knot 104 233 0.81 40 150 223 
GGGGRSVDTMALWLGLRAVLVVAGLAVLLQLIRGWLSSKSYVFNREEIARLAKEHSGLDYEVAFSKIIVELRKKHPGHILQDEDLQWVFVNAGGWMGSMCLLHASLTEYVLLFGTAVDTGGHSGRYWAEISDTILSGTFRQWKEGTTKSEIFYPGDTIVHEVGEATSVQWSSGTWMVEYGRGFIPSTLAFALADTIFSTQDFLTLFYTVKVYSKALLLEASTHLSQLGFFAAA
7GSC , Knot 141 321 0.84 40 205 309 
MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
5ULW , Knot 5 7 0.46 6 5 5 
AGGACCC

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 \(c\).

\(|P_{f(8YBB_1)}(2) \setminus P_{f(7GSC_1)}(2)|=61\), \(|P_{f(7GSC_1)}(2) \setminus P_{f(8YBB_1)}(2)|=116\). 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 1:11110010011111110111111111111011011100000110000110110000110001110011101000011011000010111101111110101101010001111101100110010011010001101010010010000011011001100110100101001011100101111001111110011000011011001010001111010001001111111
Pair \(Z_2\) Length of longest common subsequence
8YBB_1,7GSC_1 177 4
8YBB_1,5ULW_1 151 3
7GSC_1,5ULW_1 206 2

Newick tree

 
[
	7GSC_1:10.95,
	[
		8YBB_1:75.5,5ULW_1:75.5
	]:26.45
]

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 \((0.85)(0.8)(\frac{554 }{\log_{20} 554}-\frac{233}{\log_{20}233})=91.5\)
Status Protein1 Protein2 d d1/2
Query variables 8YBB_1 7GSC_1 118 99.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]