CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4PRF_1 1BCM_1 2QJB_1 Letter Amino acid
0 20 5 E Glutamic acid
26 30 5 G Glycine
0 11 4 I Isoleucine
0 16 3 F Phenylalanine
0 22 4 R Arginine
0 7 6 H Histidine
0 24 9 L Leucine
0 9 3 M Methionine
25 5 7 C Cysteine
0 20 6 D Aspartic acid
0 14 7 P Proline
0 17 3 T Threonine
0 8 2 W Tryptophan
0 12 5 Y Tyrosine
0 15 7 N Asparagine
0 9 4 Q Glutamine
0 22 9 K Lycine
0 8 8 S Serine
0 28 11 V Valine
11 30 8 A Alanine 

4PRF_1|Chain A[auth B]|Hepatitis Delta virus ribozyme|null
>1BCM_1|Chains A, B|BACTERIOPHAGE MU TRANSPOSASE|Enterobacteria phage Mu (10677)
>2QJB_1|Chains A, B|Bone morphogenetic protein 2|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 \(w=f(c)\)
4PRF , Knot 25 76 0.47 8 15 39 
GAUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGACU
1BCM , Knot 143 327 0.84 40 199 315 
HLIPAQQRTVEHLDAMQWINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTRKILGWRCDVSENIDSIRLSFMDVVTRYGIPEDFHITIDNTRGAANKWLTGGAPNRYRFKVKEDDPKGLFLLMGAKMHWTSVVAGKGWGQAKPVERAFGVGGLEEYVDKHPALAGAYTGPNPQAKPDNYGDRAVDAELFLKTLAEGVAMFNARTGRETEMCGGKLSFDDVFEREYARTIVRKPTEEQKRMLLLPAEAVNVSRKGEFTLKVGGSLKGAKNVYYNMALMNAGVKKVVVRFDPQQLHSTVYCYTLDGRFICEAECLAPVAFNDAAAGREY
2QJB , Knot 62 116 0.84 40 103 113 
MAQAKHKQRKRLKSSCKRHPLYVDFSDVGWNDWIVAPPGYHAFYCHGECPFPLADHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLYLDENEKVVLKNYQDMVVEGCGCR

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 \(c\).

\(|P_{f(4PRF_1)}(2) \setminus P_{f(1BCM_1)}(2)|=10\), \(|P_{f(1BCM_1)}(2) \setminus P_{f(4PRF_1)}(2)|=194\). 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 1:1101100110101100001100000001001101001100111011010010010100001101101110111100
Pair \(Z_2\) Length of longest common subsequence
4PRF_1,1BCM_1 204 3
4PRF_1,2QJB_1 110 4
1BCM_1,2QJB_1 198 3

Newick tree

 
[
	1BCM_1:11.63,
	[
		4PRF_1:55,2QJB_1:55
	]:56.63
]

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 \((0.85)(0.8)(\frac{403 }{\log_{20} 403}-\frac{76}{\log_{20}76})=101.\)
Status Protein1 Protein2 d d1/2
Query variables 4PRF_1 1BCM_1 139 80
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: