CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1GFA_1 2OCY_1 9BHB_1 Letter Amino acid
10 11 3 N Asparagine
9 13 8 D Aspartic acid
8 0 2 C Cysteine
5 6 4 I Isoleucine
6 10 15 S Serine
6 3 5 Y Tyrosine
8 6 9 V Valine
14 12 9 A Alanine
6 7 4 Q Glutamine
5 18 3 K Lycine
2 3 2 M Methionine
2 0 3 P Proline
5 10 5 T Threonine
14 8 8 R Arginine
3 21 7 E Glutamic acid
11 0 11 G Glycine
1 2 0 H Histidine
8 23 13 L Leucine
2 1 6 F Phenylalanine
5 0 4 W Tryptophan 

1GFA_1|Chain A|LYSOZYME|Homo sapiens (9606)
>2OCY_1|Chains A, B|Rab guanine nucleotide exchange factor SEC2|Saccharomyces cerevisiae (4932)
>9BHB_1|Chain A[auth H]|C74 heavy chain|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 \(w=f(c)\)
1GFA , Knot 68 130 0.84 40 109 128 
KDFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV
2OCY , Knot 69 154 0.75 32 98 144 
SMALSTQLIESVDKQSHLEEQLNKSLKTIASQKAAIENYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREKDTLLDTLTLQLKNLKKVMHSLDNESTV
9BHB , Knot 58 121 0.76 38 93 117 
EVQLVQSGGALVRPGGSLRLSCAASGFDFSDFEMNWVRQAPGKGLEWISYISKISAASFYADSVEGRFTISRDNTKNLLWLEMTSLRDEDTAVYYCARDLPGYLERVFDLWGQGTLVSVSS

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 \(c\).

\(|P_{f(1GFA_1)}(2) \setminus P_{f(2OCY_1)}(2)|=79\), \(|P_{f(2OCY_1)}(2) \setminus P_{f(1GFA_1)}(2)|=68\). 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 1:0010000110010011101001101101101101001000010000110000001110100001000100111101001000111000110111010011001011011111000000001000101011
Pair \(Z_2\) Length of longest common subsequence
1GFA_1,2OCY_1 147 4
1GFA_1,9BHB_1 138 3
2OCY_1,9BHB_1 127 3

Newick tree

 
[
	1GFA_1:73.69,
	[
		9BHB_1:63.5,2OCY_1:63.5
	]:10.19
]

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 \((0.85)(0.8)(\frac{284 }{\log_{20} 284}-\frac{130}{\log_{20}130})=48.0\)
Status Protein1 Protein2 d d1/2
Query variables 1GFA_1 2OCY_1 57 55.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]