CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5APO_1 1SEH_1 1WQK_1 Letter Amino acid
0 4 0 H Histidine
0 2 5 Y Tyrosine
0 11 1 V Valine
0 7 1 R Arginine
0 12 1 D Aspartic acid
917 18 8 G Glycine
0 6 2 F Phenylalanine
0 5 2 K Lycine
0 6 0 M Methionine
0 8 2 S Serine
0 7 6 T Threonine
968 12 0 A Alanine
0 4 1 N Asparagine
631 1 6 C Cysteine
0 16 1 L Leucine
0 1 1 W Tryptophan
0 7 0 Q Glutamine
0 6 0 E Glutamic acid
0 10 3 I Isoleucine
0 9 2 P Proline 

5APO_1|Chain A[auth 5]|25S ribosomal RNA|Saccharomyces cerevisiae S288c (559292)
>1SEH_1|Chain A|Deoxyuridine 5'-triphosphate nucleotidohydrolase|Escherichia coli (562)
>1WQK_1|Chain A|Toxin APETx1|Anthopleura elegantissima (6110)
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 \(w=f(c)\)
5APO , Knot 551 3396 0.44 10 19 69 
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGAAAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUGAAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCCUUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGUGCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGGGUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUGAUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGGGAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUCUCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCUUGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACGUAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGAGUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUAGGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGAGUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCCAGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCUCAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGGGUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAAUUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGGCGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCACAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGCGUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGGAGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACGUCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAGGCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAUAUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAGUUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUUAUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAAUCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAGGUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGAUCAACUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUGGUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCUAUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAUAAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAAUGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGAUCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGAUAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGGUAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUCGAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCUCUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUACCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGCGGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUCUAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUACGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGCGGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAUUUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUACGAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU
1SEH , Knot 73 152 0.80 40 118 149 
MMKKIDVKILDPRVGKEFPLPTYATSGSAGLDLRACLNDAVELAPGDTTLVPTGLAIHIADPSLAAMMLPRSGLGHKHGIVLGNLVGLIDSDYQGQLMISVWNRGQDSFTIQPGERIAQMIFVPVVQAEFNLVEDFDATDRGEGGFGHSGRQ
1WQK , Knot 24 42 0.71 30 34 40 
GTTCYCGKTIGIYWFGTKTCPSNRGYTGSCGYFLGICCYPVD

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 \(c\).

\(|P_{f(5APO_1)}(2) \setminus P_{f(1SEH_1)}(2)|=15\), \(|P_{f(1SEH_1)}(2) \setminus P_{f(5APO_1)}(2)|=114\). 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 1:100011000011100111011111010001001110001110101001101110111111111111100110011110010000110110110111011110110111110001110001111000110100000110100011100101100011111111011000011110010000001000101000000111101111010010111111011111000010101101111110101100000010111101000001111110011100100011111010110000111011101101110000100011110011101001101111110011011011101110101101101111111011111111000011111111110111111101010111100100111111111111010001100111010110100001010000001000000101110111111100001010000100111001101001100001101101111011100010111110101100010000110111010010110001011111010010011001111001111100101101011100111110100110101101100101010010001000011110101110011111100011010001010111010001110101111000101010101101111101110101110011110000101111110101011001100110000110100000111011100011101111101011001001111000111111011011100101000111011110111100111111110000110111110001011011000011010101110011001001110001110101111101111110011001110010001101100110000010011110000000011110110111110001010011000010111101111011101100111110000111100111101100001100010000011100001110101011111100000100100011001110101110100011101111110000011011100100000110111011110011011010111101110011101011110011110100111101010100010011101001011111101001100010001110110011101101100101111100111100010011111101010110110001001100111011100110000111110111011010001110101001000101000010010011110011010110100001101110111011101011111001101101111000111001011110011100111011000001101011100001101101101101110100011101111100001111100111101111111110000101001101101100111010111001100110000111111011111110000100001111100011000010101110010010011111111100011001111000011110001110101110000001011011010110011101011111010011010111000011111111001000000000000110110001001000011110011000100011111011110000101100111111110011010000010011000011010100010110110001011111000101111111110110000010100111001010011011001011011100000111101110110000011001101111011010111011111111001101111011100010110000111101111100110000111110011000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111111111111111111110110011000111100110101110111111110001100100011001111010110100101101100111111011010011010110101100000100011010000111010011110111111100011001110101110111011011111011001011000000011110110011101000010010001100110110101010111011100110111100000100100000100010010001101111001011001111111011100011011110011011111111111100001001110001100001100011010010111111101011111101011110111011111000011010011011110100100100000101100000001000100011011110111100111100010000001010000110100011110000100011110011000111001111101001001110111111000110011110110101000100111011011010111010000111111110001011111101111100000110111101111111011111000000011000011000001101011101011100101111101011000100110000001100000011110001111001111101001111111001001011111011001100010110110011101000101101101001000000110000001101001100000000100101001111011110001101110100111001000100010011011111101011100111000111001001011110111001100001000010011011101001001011011011001110001101011111111011000100011101100110000010110010001100111010010010111100100100010011100101100111010000011100111100010100111101011011000000010000101011010111011101011101111010000010110100100111001011011100110110110101000110111111100001110100010011011100101101001000010101111101110010001010101100011101010110111101001011101101111011000010010010110001001111001110000010010001100010
Pair \(Z_2\) Length of longest common subsequence
5APO_1,1SEH_1 129 2
5APO_1,1WQK_1 49 2
1SEH_1,1WQK_1 128 3

Newick tree

 
[
	1SEH_1:72.82,
	[
		5APO_1:24.5,1WQK_1:24.5
	]:48.32
]

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 \((0.85)(0.8)(\frac{3548 }{\log_{20} 3548}-\frac{152}{\log_{20}152})=822.\)
Status Protein1 Protein2 d d1/2
Query variables 5APO_1 1SEH_1 547 309.5
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: