CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2HBB_1 2OKR_1 7SPY_1 Letter Amino acid
7 25 25 A Alanine
0 19 14 R Arginine
2 15 9 Q Glutamine
1 15 10 Y Tyrosine
4 14 19 N Asparagine
2 27 27 D Aspartic acid
0 4 7 C Cysteine
3 24 20 E Glutamic acid
1 19 24 T Threonine
5 16 20 G Glycine
1 17 16 P Proline
0 21 28 S Serine
0 5 3 W Tryptophan
0 13 6 H Histidine
3 22 23 I Isoleucine
5 44 32 L Leucine
10 19 19 K Lycine
1 12 15 M Methionine
3 13 20 F Phenylalanine
3 22 20 V Valine 

2HBB_1|Chain A|50S ribosomal protein L9|Geobacillus stearothermophilus (1422)
>2OKR_1|Chains A, C[auth D]|Mitogen-activated protein kinase 14|Homo sapiens (9606)
>7SPY_1|Chain A|ATPase ASNA1 homolog|Giardia intestinalis (strain ATCC 50803 / WB clone C6) (184922)
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 \(w=f(c)\)
2HBB , Knot 30 51 0.77 30 43 48 
MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEATPANLKALEAQK
2OKR , Knot 162 366 0.87 40 225 352 
GSHMLEMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
7SPY , Knot 155 357 0.85 40 216 345 
ATYMLPSLHDILDQHTYKWIFFGGKGGVGKTTTSSSFSVLMAETRPNEKFLLLSTNPAHNISDAFDQKFGKAPTQVSGIPNLYAMEVDASNEMKSAVEAVQKETGSAADNDAESKSEGDMFGGLNDLITCASSFIKDGTFPGMDEMWSFINLIKLIDTNEYSTVIFDTAPTGHTLRFLELPETVNKVLEIFTRLKDNMGGMLSMVMQTMGLSQNDIFGLIDKTYPKIDVVKRISAEFRDPSLCTFVGVCIPEFLSLYETERLVQRLAVLDMDCHAIVINFVLDANAATPCSMCRSRARMQNKYIDQINELYDDFNIVLSPLRHDEVRGIANLRDYAETLIKPYRFCWSANPDPSSAK

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 \(c\).

\(|P_{f(2HBB_1)}(2) \setminus P_{f(2OKR_1)}(2)|=17\), \(|P_{f(2OKR_1)}(2) \setminus P_{f(2HBB_1)}(2)|=199\). 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 1:101111001010100101001101010011100111101011010110100
Pair \(Z_2\) Length of longest common subsequence
2HBB_1,2OKR_1 216 3
2HBB_1,7SPY_1 201 3
2OKR_1,7SPY_1 171 3

Newick tree

 
[
	2HBB_1:10.87,
	[
		7SPY_1:85.5,2OKR_1:85.5
	]:24.37
]

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 \((0.85)(0.8)(\frac{417 }{\log_{20} 417}-\frac{51}{\log_{20}51})=114.\)
Status Protein1 Protein2 d d1/2
Query variables 2HBB_1 2OKR_1 148 83.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: