CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8CQS_1 1FYG_1 6YWL_1 Letter Amino acid
16 3 14 K Lycine
16 0 22 V Valine
10 1 16 N Asparagine
13 0 9 D Aspartic acid
5 0 7 E Glutamic acid
6 1 7 Y Tyrosine
2 0 7 H Histidine
9 1 6 I Isoleucine
16 3 10 S Serine
21 0 19 L Leucine
7 0 3 M Methionine
5 0 5 F Phenylalanine
8 1 5 P Proline
7 1 6 T Threonine
26 3 15 A Alanine
1 6 3 C Cysteine
11 0 3 Q Glutamine
8 2 2 R Arginine
14 3 14 G Glycine
1 0 0 W Tryptophan 

8CQS_1|Chains A, B|Nitroreductase-like protein|Bacteroides thetaiotaomicron (818)
>1FYG_1|Chain A|OMEGA CONOTOXIN SO3|null
>6YWL_1|Chains A, B, C, D, E|NSP3 macrodomain|Severe acute respiratory syndrome coronavirus 2 (2697049)
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 \(w=f(c)\)
8CQS , Knot 94 202 0.82 40 144 195 
AGLEVLFQGPADKVVKLPKPNLNRTGTVMKALSERQSTREYASKALTLADLSDLLWAANGINRSDAGKRTAPSAMNKQDVDVYVILSEGSYLYDAKNHQLNLIAEGDYRGAVAGGQAFVKTAPVSLVLISDVSRFGDAQKIQNQLMGAMDAGIVSQNISIFCSAAKLATVPRASMDAAQLKKVLKLKDSQIPMMNHPVGYFK
1FYG , Knot 16 25 0.68 22 23 23 
CKAAGKPCSRIAYNCCTGSCRSGKC
6YWL , Knot 84 173 0.83 38 122 166 
GHMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMK

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 \(c\).

\(|P_{f(8CQS_1)}(2) \setminus P_{f(1FYG_1)}(2)|=133\), \(|P_{f(1FYG_1)}(2) \setminus P_{f(8CQS_1)}(2)|=12\). 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 1:1110111011100110110101000101101100000000010011011010011111011000011000110110000101011100100100100001011101000111111011100111011110010011010010001111101111000101100110110110101011010011010000111100111010
Pair \(Z_2\) Length of longest common subsequence
8CQS_1,1FYG_1 145 3
8CQS_1,6YWL_1 144 3
1FYG_1,6YWL_1 127 3

Newick tree

 
[
	8CQS_1:74.94,
	[
		6YWL_1:63.5,1FYG_1:63.5
	]:11.44
]

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 \((0.85)(0.8)(\frac{227 }{\log_{20} 227}-\frac{25}{\log_{20}25})=69.4\)
Status Protein1 Protein2 d d1/2
Query variables 8CQS_1 1FYG_1 89 49
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]