CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7KSC_1 1BIM_1 2ZNV_1 Letter Amino acid
8 6 9 C Cysteine
6 22 12 I Isoleucine
3 17 2 Y Tyrosine
6 23 13 V Valine
13 16 8 A Alanine
2 12 5 N Asparagine
7 29 13 T Threonine
3 17 9 D Aspartic acid
6 15 12 K Lycine
0 6 13 H Histidine
5 26 21 L Leucine
8 13 9 P Proline
2 12 6 Q Glutamine
0 16 10 E Glutamic acid
1 8 4 M Methionine
0 19 7 F Phenylalanine
11 33 8 S Serine
0 3 1 W Tryptophan
4 10 5 R Arginine
8 34 11 G Glycine 

7KSC_1|Chains A, B, C, D|Non-specific lipid-transfer protein|Punica granatum (22663)
>1BIM_1|Chains A, B|Renin|Homo sapiens (9606)
>2ZNV_1|Chains A, D|AMSH-like protease|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 \(w=f(c)\)
7KSC , Knot 45 93 0.73 32 74 88 
AVTCGQVASSLAPCIPYARSAGGAVPPACCSGIKTLDGMARTTPDRQATCKCLKSASTSISGINYGLVASLPAKCGVNIPYKISPSTDCARVK
1BIM , Knot 146 337 0.84 40 205 322 
GNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR
2ZNV , Knot 86 178 0.83 40 135 174 
GPGHMEGLRCVVLPEDLCHKFLQLAESNTVRGIATCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHKDTGIFRLTNAGMLEVSACKKKGFHPHTKEPRLFSICKHVLVKDIKIIVLDLR

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 \(c\).

\(|P_{f(7KSC_1)}(2) \setminus P_{f(1BIM_1)}(2)|=26\), \(|P_{f(1BIM_1)}(2) \setminus P_{f(7KSC_1)}(2)|=157\). 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 1:110010110011101101001111111100011001011100010001000010010001011001111011100110110010100001010
Pair \(Z_2\) Length of longest common subsequence
7KSC_1,1BIM_1 183 3
7KSC_1,2ZNV_1 161 3
1BIM_1,2ZNV_1 176 3

Newick tree

 
[
	1BIM_1:92.65,
	[
		7KSC_1:80.5,2ZNV_1:80.5
	]:12.15
]

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 \((0.85)(0.8)(\frac{430 }{\log_{20} 430}-\frac{93}{\log_{20}93})=102.\)
Status Protein1 Protein2 d d1/2
Query variables 7KSC_1 1BIM_1 132 83
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: