CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5HPI_1 5LQT_1 6EKR_1 Letter Amino acid
3 0 23 F Phenylalanine
13 0 14 T Threonine
6 0 16 Y Tyrosine
10 0 12 N Asparagine
11 0 15 E Glutamic acid
6 0 11 H Histidine
11 0 30 S Serine
11 0 10 Q Glutamine
4 0 18 K Lycine
9 0 11 P Proline
2 0 7 M Methionine
17 0 16 V Valine
7 0 23 D Aspartic acid
3 4 5 C Cysteine
6 5 15 G Glycine
27 0 24 L Leucine
1 0 3 W Tryptophan
14 1 16 A Alanine
9 0 16 R Arginine
8 0 27 I Isoleucine 

5HPI_1|Chains A, B, C, D|p-hydroxybenzoate hydroxylase transcriptional activator|Acinetobacter baylyi str. ADP1 (62977)
>5LQT_1|Chains A, B|RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*CP*GP*GP*C)-3')|Homo sapiens (9606)
>6EKR_1|Chain A|Type ii site-specific deoxyribonuclease|Klebsiella pneumoniae (573)
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 \(w=f(c)\)
5HPI , Knot 79 178 0.76 40 119 170 
SNAAHLPKVAQSFLNLLCAQTSLTFSIVVLDEHEVVPVARSYLPQQDNRVSPYGMHLGNRLPAHATSTGKVLLSVLDREVQIEWIEKYGLKRLTPYTITDEHTFLETLDAVRQSDYCLSTEEHELGVIAIAVPVLNAQGLTIAALNCMSQTNRVQPQYLIDQVLPLLRNTANELRNLV
5LQT , Knot 5 10 0.38 6 6 7 
GCCGGACGGC
6EKR , Knot 135 312 0.82 40 195 296 
MDILKEKIDVASRLYNLNLDHIPATLQVIEHAMLLLKNNAGYGYFGSFNGKNTQEYHSFTFNGEYSRPVRDDLFITDYDFFVSGFREFNESLRDIGSKWSSFDSRRANKIIYTSVMSVACCFDLWKSGSRKTPGTFFEIFMAAVLKWMIPDEIFSKHIPLIDQLESDDESIDPSSVSTDIVIKSAYANASVVIPLKITTRERIVQPFAQQRILDSYFGNGVYFSFLACISETQQDKKKKKVNHICVPGTIRLYQKYLSSLSGMYYCDIPERYLERDLTDIIPVRTMGDFLFDIYSFFRSQGAAALEHHHHHH

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 \(c\).

\(|P_{f(5HPI_1)}(2) \setminus P_{f(5LQT_1)}(2)|=119\), \(|P_{f(5LQT_1)}(2) \setminus P_{f(5HPI_1)}(2)|=6\). 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 1:0011011011001101101000101011110000111110001100000101011011001110100010111011000101011000110010100100000110010110000001000000111111111110101101111001000001010011001111100010010011
Pair \(Z_2\) Length of longest common subsequence
5HPI_1,5LQT_1 125 1
5HPI_1,6EKR_1 162 4
5LQT_1,6EKR_1 195 2

Newick tree

 
[
	6EKR_1:97.00,
	[
		5HPI_1:62.5,5LQT_1:62.5
	]:34.50
]

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 \((0.85)(0.8)(\frac{188 }{\log_{20} 188}-\frac{10}{\log_{20}10})=64.2\)
Status Protein1 Protein2 d d1/2
Query variables 5HPI_1 5LQT_1 78 41
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]