CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8EOK_1 8OKN_1 8RXA_1 Letter Amino acid
28 11 5 R Arginine
33 11 6 I Isoleucine
12 10 3 M Methionine
4 3 0 W Tryptophan
40 9 10 E Glutamic acid
56 29 18 L Leucine
24 17 4 F Phenylalanine
49 16 7 S Serine
48 24 3 T Threonine
73 27 3 V Valine
32 17 2 A Alanine
3 12 2 C Cysteine
36 14 4 Q Glutamine
46 26 2 G Glycine
10 7 8 H Histidine
39 11 10 K Lycine
38 13 4 P Proline
23 11 5 Y Tyrosine
23 21 8 N Asparagine
28 17 5 D Aspartic acid 

8EOK_1|Chain A[auth G]|Complement C3 beta chain|Homo sapiens (9606)
>8OKN_1|Chains A, B|3C-like proteinase nsp5|Severe acute respiratory syndrome coronavirus 2 (2697049)
>8RXA_1|Chains A, B|AP2 domain transcription factor AP2-O5, putative|Plasmodium falciparum 3D7 (36329)
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 \(w=f(c)\)
8EOK , Knot 246 645 0.82 40 268 586 
SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNHMGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPGSTVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMGQWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYGKKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGKSLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGSPAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLKAGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGSLVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEKADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQPAA
8OKN , Knot 134 306 0.83 40 196 290 
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ
8RXA , Knot 54 109 0.77 38 86 103 
MDEYKTNFIDLTREALSLILQDLKNNVIPKIPVGIEKRERYKNSLRLCLKSARNTQHMNELEPYLELFSECIKNSKLPSHMSLKDQLFYLDKLLENLYFQGVEHHHHHH

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 \(c\).

\(|P_{f(8EOK_1)}(2) \setminus P_{f(8OKN_1)}(2)|=123\), \(|P_{f(8OKN_1)}(2) \setminus P_{f(8EOK_1)}(2)|=51\). 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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
Pair \(Z_2\) Length of longest common subsequence
8EOK_1,8OKN_1 174 5
8EOK_1,8RXA_1 214 3
8OKN_1,8RXA_1 192 3

Newick tree

 
[
	8RXA_1:10.08,
	[
		8EOK_1:87,8OKN_1:87
	]:19.08
]

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 \((0.85)(0.8)(\frac{951 }{\log_{20} 951}-\frac{306}{\log_{20}306})=173.\)
Status Protein1 Protein2 d d1/2
Query variables 8EOK_1 8OKN_1 220 161.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]