CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7WVM_1 5XYH_1 3HFJ_1 Letter Amino acid
4 9 19 E Glutamic acid
0 11 6 H Histidine
5 18 12 K Lycine
6 24 13 Y Tyrosine
5 40 8 A Alanine
2 4 2 C Cysteine
3 25 13 I Isoleucine
10 29 22 L Leucine
10 27 12 V Valine
5 14 9 R Arginine
5 15 6 Q Glutamine
17 46 12 G Glycine
2 5 4 M Methionine
2 28 13 P Proline
8 28 11 T Threonine
5 28 6 N Asparagine
5 22 5 D Aspartic acid
6 9 7 F Phenylalanine
13 34 9 S Serine
4 9 2 W Tryptophan 

7WVM_1|Chains A, D[auth C]|Heavy Chain of Cemiplimab|Homo sapiens (9606)
>5XYH_1|Chain A|CbsA|Xanthomonas oryzae pv. oryzae (64187)
>3HFJ_1|Chains A, B|Nicotinate (Nicotinamide) nucleotide adenylyltransferase|Bacillus anthracis (1392)
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 \(w=f(c)\)
7WVM , Knot 59 117 0.80 38 91 114 
EVQLLESGGVLVQPGGSLRLSCAASGFTFSNFGMTWVRQAPGKGLEWVSGISGGGRDTYFADSVKGRFTISRDNSKNTLYLQMNSLKGEDTAVYYCVKWGNIYFDYWGQGTLVTVSS
5XYH , Knot 175 425 0.83 40 219 396 
QSHVDNPFVGASGYVNPDYSKEVDSSIVKVKDVQLKAKMQVVKSYPTYVWLDSIDAIYGGSRNAGRLSLQGHLNAALAQKKANTPITVGLVIYDMPGRDCHALASNGELPLTQAGLQRYKTEYIDVIASTLANPKYKGLRIVNIIEPDSLPNLVTNQSTPACGQASSSGIYEAGIKYALDKLHAIPNVYNYMDIGHSGWLAWRSNMTPAISLYTRVVQGTAAGLASADGFITNTANYTPLHEPNLPNPDLTIGGQPISSSTFYQWNSVFDESTYAEVLYNAFVGAGWPSKIGFLIDTGRNGWGGSARPTSASGNDVNTYVNSGRVDRRLHRGNWCNQSGAGIGMPPTAAPGGHIHAYVWGKGGGESDGSSKYIPNKQGKGFDRYCDPTYTTPDGTLTGALPNAPIAGTWFHAHFVQLVTNAYPAI
3HFJ , Knot 93 191 0.85 40 145 185 
GAMRKIGIIGGTFDPPHYGHLLIANEVYHALNLEEVWFLPNQIPPHKQGRNITSVESRLQMLELATEAEEHFSICLEELSRKGPSYTYDTMLQLTKKYPDVQFHFIIGGDMVEYLPKWYNIEALLDLVTFVGVARPGYKLRTPYPITTVEIPEFAVSSSLLRERYKEKKTCKYLLPEKVQVYIERNGLYES

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 \(c\).

\(|P_{f(7WVM_1)}(2) \setminus P_{f(5XYH_1)}(2)|=27\), \(|P_{f(5XYH_1)}(2) \setminus P_{f(7WVM_1)}(2)|=155\). 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 1:010110011111011101010011011010011101100111011011011011100001100101010100000000101010010100011000101101010011010110100
Pair \(Z_2\) Length of longest common subsequence
7WVM_1,5XYH_1 182 3
7WVM_1,3HFJ_1 156 3
5XYH_1,3HFJ_1 162 3

Newick tree

 
[
	5XYH_1:88.69,
	[
		7WVM_1:78,3HFJ_1:78
	]:10.69
]

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 \((0.85)(0.8)(\frac{542 }{\log_{20} 542}-\frac{117}{\log_{20}117})=125.\)
Status Protein1 Protein2 d d1/2
Query variables 7WVM_1 5XYH_1 161 101.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]