CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1TLD_1 9JLU_1 7GCO_1 Letter Amino acid
16 23 21 N Asparagine
14 50 29 L Leucine
3 29 17 F Phenylalanine
8 20 13 P Proline
17 29 27 V Valine
2 21 11 R Arginine
10 9 14 Q Glutamine
25 17 26 G Glycine
2 7 10 M Methionine
10 29 11 Y Tyrosine
6 24 17 D Aspartic acid
3 8 7 H Histidine
14 47 11 K Lycine
14 23 17 A Alanine
12 3 12 C Cysteine
4 60 9 E Glutamic acid
15 28 11 I Isoleucine
34 18 16 S Serine
10 18 24 T Threonine
4 14 3 W Tryptophan 

1TLD_1|Chain A|BETA-TRYPSIN|Bos taurus (9913)
>9JLU_1|Chain A|Glycoside hydrolase family 57 N-terminal domain-containing protein|Aquifex aeolicus VF5 (224324)
>7GCO_1|Chain A|3C-like proteinase|Severe acute respiratory syndrome coronavirus 2 (2697049)
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 \(w=f(c)\)
1TLD , Knot 101 223 0.81 40 140 216 
IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN
9JLU , Knot 188 477 0.81 40 223 431 
MKKLFLVFWWHMHQPLYREPYTGEYLLPWTFFHAVKDYYDMPAYLKDFEIKLNFNLTPVLIDQIQEYAQGKAKDVFLEAIRKDPDDLEKEEVEKLIEFTKLNYEKPIYRFERIRELMNKEKLNREELLDLQTLNLLAWCGRTLRKDLKDLLNKGRNYTQEEKEYVLNKYFEIIKKTLSIYREIKEEGKGSVSTSPYYHPLIPILLNPNCVYETTPNVKIPDFAVSFREDASKHVELAKEKYFEIFGEHPVYMWPPEASVSNEALELYYEKGINMLATDEVILKNSVERASPYLRYYFRELISVFFRDKTLSDLIGFSYHAWNAEDAVRDFIGRLKKIHESVDFQPVVFVVLNGENCWEYYEENGIPFLEKLYSTLEKEEWIETLTLEEAMRKEDVKTEVIESVKAGTWFDGNFLKWIGNKEKNEYWKILIEAKKKAKNDYILVAEGSDWFWWQGEEKAPFVEVFDKLFRSFVRRAQE
7GCO , Knot 134 306 0.83 40 196 290 
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

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 \(c\).

\(|P_{f(1TLD_1)}(2) \setminus P_{f(9JLU_1)}(2)|=69\), \(|P_{f(9JLU_1)}(2) \setminus P_{f(1TLD_1)}(2)|=152\). 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 1:1111000110011001010010010110110001110110000011010110001011010001101000110100000010001111010011010001101011000101100011011100000100010110010111100000001011010001101101011000001001111100101011101101010000111000100010110001100
Pair \(Z_2\) Length of longest common subsequence
1TLD_1,9JLU_1 221 3
1TLD_1,7GCO_1 184 3
9JLU_1,7GCO_1 191 4

Newick tree

 
[
	9JLU_1:10.76,
	[
		1TLD_1:92,7GCO_1:92
	]:14.76
]

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 \((0.85)(0.8)(\frac{700 }{\log_{20} 700}-\frac{223}{\log_{20}223})=133.\)
Status Protein1 Protein2 d d1/2
Query variables 1TLD_1 9JLU_1 171 126.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]