CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1IBJ_1 9CSH_1 5JPJ_1 Letter Amino acid
39 7 3 A Alanine
27 6 6 D Aspartic acid
27 8 10 G Glycine
9 3 6 Y Tyrosine
27 17 10 T Threonine
18 7 3 R Arginine
5 1 2 C Cysteine
13 6 6 Q Glutamine
22 9 4 E Glutamic acid
25 6 5 I Isoleucine
44 24 5 L Leucine
21 16 6 P Proline
18 7 5 N Asparagine
30 3 3 K Lycine
19 5 3 F Phenylalanine
54 16 22 S Serine
13 13 2 H Histidine
13 0 1 M Methionine
3 1 1 W Tryptophan
37 4 8 V Valine 

1IBJ_1|Chains A, B[auth C]|CYSTATHIONINE BETA-LYASE|Arabidopsis thaliana (3702)
>9CSH_1|Chains A, C|Methyltransferase/Protease/Ubiquitinyl hydrolase|Turnip yellow mosaic virus (12154)
>5JPJ_1|Chains A, B|6aJL2 protein|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 \(w=f(c)\)
1IBJ , Knot 190 464 0.83 40 229 441 
MTSSLSLHSSFVPSFADLSDRGLISKNSPTSVSISKVPTWEKKQISNRNSFKLNCVMEKSVDGQTHSTVNNTTDSLNTMNIKEEASVSTLLVNLDNKFDPFDAMSTPLYQTATFKQPSAIENGPYDYTRSGNPTRDALESLLAKLDKADRAFCFTSGMAALSAVTHLIKNGEEIVAGDDVYGGSDRLLSQVVPRSGVVVKRVNTTKLDEVAAAIGPQTKLVWLESPTNPRQQISDIRKISEMAHAQGALVLVDNSIMSPVLSRPLELGADIVMHSATKFIAGHSDVMAGVLAVKGEKLAKEVYFLQNSEGSGLAPFDCWLCLRGIKTMALRIEKQQENARKIAMYLSSHPRVKKVYYAGLPDHPGHHLHFSQAKGAGSVFSFITGSVALSKHLVETTKYFSIAVSFGSVKSLISMPCFMSHASIPAEVREARGLTEDLVRISAGIEDVDDLISDLDIAFKTFPL
9CSH , Knot 75 159 0.79 38 112 152 
HHHHHHGSSQLLPAPLTNDPTAIGPVLPFEELHPRRYPENTATFLTRLRSLPSNHLPQPTLNCLLSAVSDQTKVSEEHLWESLQTILPDSQLSNEETNTLGLSTEHLTALAHLYNFQATVYSDRGPILFGPSDTIKRIDITHTTGPPSHFSPGKRLLGS
5JPJ , Knot 56 111 0.79 40 82 102 
NFMLTQPHSVSESPGKTVTISCTGSSGSIASNYVQWYQQRPGSSPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSNHVVFGGGTKLTVL

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 \(c\).

\(|P_{f(1IBJ_1)}(2) \setminus P_{f(9CSH_1)}(2)|=143\), \(|P_{f(9CSH_1)}(2) \setminus P_{f(1IBJ_1)}(2)|=26\). 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 1:10001010001110110100011100001001010011010000100000101001100010100000100000010010100010100111010001011011001100010100101100110000001010001100111010010011010011111011001100100111100101100011001110011110010000100111111100011110010010001001001001101011111100011011100110111011100100111100011111111010011001011000010111110011010110011101000000100111010001010010011110011001010010111011011010111000110000010111011010011011011001011101001011000110101110010011001011100111
Pair \(Z_2\) Length of longest common subsequence
1IBJ_1,9CSH_1 169 4
1IBJ_1,5JPJ_1 203 3
9CSH_1,5JPJ_1 132 4

Newick tree

 
[
	1IBJ_1:10.87,
	[
		9CSH_1:66,5JPJ_1:66
	]:34.87
]

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 \((0.85)(0.8)(\frac{623 }{\log_{20} 623}-\frac{159}{\log_{20}159})=133.\)
Status Protein1 Protein2 d d1/2
Query variables 1IBJ_1 9CSH_1 168 109.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]