CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7HWQ_1 8VTE_1 1GNI_1 Letter Amino acid
9 10 36 D Aspartic acid
7 11 62 E Glutamic acid
3 3 1 W Tryptophan
14 17 41 V Valine
10 13 62 A Alanine
5 6 8 I Isoleucine
2 14 59 K Lycine
2 1 6 M Methionine
6 18 28 T Threonine
8 12 18 Y Tyrosine
9 6 24 R Arginine
6 5 35 C Cysteine
5 14 20 Q Glutamine
12 16 61 L Leucine
3 8 31 F Phenylalanine
5 9 17 N Asparagine
14 12 12 G Glycine
6 2 16 H Histidine
4 12 24 P Proline
14 31 24 S Serine 

7HWQ_1|Chain A|Protease 2A|Coxsackievirus A16 (31704)
>8VTE_1|Chains A, C|Tiragolumab antibody light chain variable domains|Mus musculus (10090)
>1GNI_1|Chain A|SERUM ALBUMIN|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 \(w=f(c)\)
7HWQ , Knot 70 144 0.80 40 112 139 
SGAIYVGNYRVVNRHLATHNDWANLVWEDSSRDLLVSSTTAQGCDTIARCDCQTGVYYCSSRRKHYPVSFSKPSLIFVEASEYYPARYQSHLMLAVGHSEPGDCGGILRCQHGVVGIVSTGGNGLVGFADVRDLLWLDEEAMEQ
8VTE , Knot 103 220 0.84 40 157 213 
DIVMTQSPDSLAVSLGERATINCKSSQTVLYSSNNKKYLAWYQQKPGQPPNLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTPFTFGPGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
1GNI , Knot 229 585 0.83 40 238 530 
DAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL

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 \(c\).

\(|P_{f(7HWQ_1)}(2) \setminus P_{f(8VTE_1)}(2)|=63\), \(|P_{f(8VTE_1)}(2) \setminus P_{f(7HWQ_1)}(2)|=108\). 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 1:011101100011000110000110111000000111000010100011000000110000000000110100101111010000110000011111100011001111000011111100110111111010011110001100
Pair \(Z_2\) Length of longest common subsequence
7HWQ_1,8VTE_1 171 4
7HWQ_1,1GNI_1 220 3
8VTE_1,1GNI_1 161 4

Newick tree

 
[
	7HWQ_1:10.82,
	[
		8VTE_1:80.5,1GNI_1:80.5
	]:23.32
]

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 \((0.85)(0.8)(\frac{364 }{\log_{20} 364}-\frac{144}{\log_{20}144})=66.7\)
Status Protein1 Protein2 d d1/2
Query variables 7HWQ_1 8VTE_1 86 71
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]