CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2XTT_1 4NBN_1 2MDL_1 Letter Amino acid
2 15 3 R Arginine
4 17 1 G Glycine
0 13 1 I Isoleucine
0 25 1 L Leucine
2 20 5 K Lycine
1 18 0 V Valine
2 18 0 A Alanine
0 18 3 F Phenylalanine
3 14 1 T Threonine
1 6 0 M Methionine
2 19 0 D Aspartic acid
3 7 0 Q Glutamine
1 17 2 H Histidine
1 17 0 S Serine
1 2 1 W Tryptophan
1 11 0 N Asparagine
3 17 1 E Glutamic acid
3 9 2 P Proline
0 10 1 Y Tyrosine
6 9 2 C Cysteine 

2XTT_1|Chain A|PROTEASE INHIBITOR SGPI-1|SCHISTOCERCA GREGARIA (7010)
>4NBN_1|Chains A, B|Caspase-6|Homo sapiens (9606)
>2MDL_1|Chain A|Anti-lipopolysaccharide factor|Scylla serrata (6761)
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 \(w=f(c)\)
2XTT , Knot 24 36 0.79 32 35 34 
EQECEPGQTKKQDCNTCRCGSDGVWACTRMGCPPHA
4NBN , Knot 128 282 0.85 40 187 273 
MGSAFYKREMFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQAARGNQHDVPVIPLDVVDNQTEKLDTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPKSNGNSHHHHHH
2MDL , Knot 15 24 0.66 26 20 22 
TCHIRRKPKFRKFKLYHEGKFWCP

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 \(c\).

\(|P_{f(2XTT_1)}(2) \setminus P_{f(4NBN_1)}(2)|=22\), \(|P_{f(4NBN_1)}(2) \setminus P_{f(2XTT_1)}(2)|=174\). 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 1:000001100000000000010011110001101101
Pair \(Z_2\) Length of longest common subsequence
2XTT_1,4NBN_1 196 3
2XTT_1,2MDL_1 51 2
4NBN_1,2MDL_1 181 3

Newick tree

 
[
	4NBN_1:10.91,
	[
		2XTT_1:25.5,2MDL_1:25.5
	]:82.41
]

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 \((0.85)(0.8)(\frac{318 }{\log_{20} 318}-\frac{36}{\log_{20}36})=91.9\)
Status Protein1 Protein2 d d1/2
Query variables 2XTT_1 4NBN_1 120 67
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: