CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2ASJ_1 2HEC_1 4OHQ_1 Letter Amino acid
0 14 6 R Arginine
0 10 9 N Asparagine
7 11 29 G Glycine
0 2 1 M Methionine
0 2 10 F Phenylalanine
0 6 4 Y Tyrosine
0 6 7 Q Glutamine
0 4 17 I Isoleucine
0 8 15 L Leucine
0 2 6 P Proline
0 9 28 V Valine
2 15 26 A Alanine
0 3 19 E Glutamic acid
0 1 3 H Histidine
0 5 22 K Lycine
0 6 21 S Serine
0 5 6 W Tryptophan
0 8 14 D Aspartic acid
0 8 4 C Cysteine
4 5 9 T Threonine 

2ASJ_1|Chains A[auth D], C[auth H]|5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3'|
>2HEC_1|Chain A|LYSOZYME|Homo sapiens (9606)
>4OHQ_1|Chains A, B|Triosephosphate isomerase, chloroplastic|Arabidopsis thaliana (3702)
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 \(w=f(c)\)
2ASJ , Knot 6 13 0.39 6 8 9 
GGTTGGATGGTAG
2HEC , Knot 67 130 0.83 40 109 128 
KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGAFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV
4OHQ , Knot 114 256 0.82 40 161 245 
MAGSGKFFVGGNWKCNGTKDSIAKLISDLNSATLEADVDVVVSPPFVYIDQVKSSLTDRIDISGQNSWVGKGGAFTGEISVEQLKDLGCKWVILGHSERRHVIGEKDEFIGKKAAYALSEGLGVIACIGEKLEEREAGKTFDVCFAQLKAFADAVPSWDNIVVAYEPVWAIGTGKVASPQQAQEVHVAVRGWLKKNVSEEVASKTRIIYGGSVNGGNSAELAKEEDIDGFLVGGASLKGPEFATIVNSVTSKKVAA

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 \(c\).

\(|P_{f(2ASJ_1)}(2) \setminus P_{f(2HEC_1)}(2)|=5\), \(|P_{f(2HEC_1)}(2) \setminus P_{f(2ASJ_1)}(2)|=106\). 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 1:1100111011011
Pair \(Z_2\) Length of longest common subsequence
2ASJ_1,2HEC_1 111 2
2ASJ_1,4OHQ_1 157 3
2HEC_1,4OHQ_1 176 4

Newick tree

 
[
	4OHQ_1:90.79,
	[
		2ASJ_1:55.5,2HEC_1:55.5
	]:35.29
]

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 \((0.85)(0.8)(\frac{143 }{\log_{20} 143}-\frac{13}{\log_{20}13})=48.3\)
Status Protein1 Protein2 d d1/2
Query variables 2ASJ_1 2HEC_1 65 35
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: