CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8HCN_1 8ICP_1 6WDN_1 Letter Amino acid
4 0 17 D Aspartic acid
6 1 17 G Glycine
2 0 10 H Histidine
6 0 16 I Isoleucine
5 0 14 M Methionine
3 0 31 F Phenylalanine
6 0 5 P Proline
9 4 11 A Alanine
0 0 4 W Tryptophan
1 0 8 Y Tyrosine
5 2 22 T Threonine
0 1 4 C Cysteine
11 0 33 E Glutamic acid
7 0 18 R Arginine
2 0 17 Q Glutamine
12 0 33 L Leucine
5 0 21 S Serine
9 0 13 V Valine
2 0 10 N Asparagine
5 0 31 K Lycine 

8HCN_1|Chains A, E, I|Urease subunit gamma|Klebsiella pneumoniae (573)
>8ICP_1|Chain A[auth T]|DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3')|
>6WDN_1|Chain A|Calcium uptake protein 2, mitochondrial|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 \(w=f(c)\)
8HCN , Knot 51 100 0.78 36 79 96 
MELTPREKDKLLLFTAALVAERRLARGLKLNYPESVALISAFIMEGARDGKSVASLMEEGRHVLTREQVMEGVPEMIPDIQVEATFPDGSKLVTVHNPII
8ICP , Knot 6 8 0.52 8 7 6 
CATTAGAA
6WDN , Knot 145 335 0.84 40 195 320 
SLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMERKTSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKLQKIISKQDDLMTVKTNETGYQEAIVKEPEINTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFSKGLSFMRKEDFAEWLLFFTNTENKDIYWKNVREKLSAGESISLDEFKSFCHFTTHLEDFAIAMQMFSLAHRPVRLAEFKRAVKVATGQELSNNILDTVFKIFDLDGDECLSHEEFLGVLKNRMHRGLWVPQHQSIQEYWKCVKKES

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 \(c\).

\(|P_{f(8HCN_1)}(2) \setminus P_{f(8ICP_1)}(2)|=75\), \(|P_{f(8ICP_1)}(2) \setminus P_{f(8HCN_1)}(2)|=3\). 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 1:1010100000111101111100011011010010011110111101100100110110010011000011011101110101010110100110100111
Pair \(Z_2\) Length of longest common subsequence
8HCN_1,8ICP_1 78 2
8HCN_1,6WDN_1 164 3
8ICP_1,6WDN_1 194 3

Newick tree

 
[
	6WDN_1:10.23,
	[
		8HCN_1:39,8ICP_1:39
	]:62.23
]

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 \((0.85)(0.8)(\frac{108 }{\log_{20} 108}-\frac{8}{\log_{20}8})=39.1\)
Status Protein1 Protein2 d d1/2
Query variables 8HCN_1 8ICP_1 48 25.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: