CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3UYY_1 8AEM_1 1CXH_1 Letter Amino acid
12 9 26 Q Glutamine
22 19 37 I Isoleucine
22 11 56 T Threonine
5 5 13 W Tryptophan
15 23 33 Y Tyrosine
33 15 65 A Alanine
6 2 3 C Cysteine
36 14 65 G Glycine
31 30 38 L Leucine
18 13 32 F Phenylalanine
20 14 28 P Proline
18 15 47 S Serine
19 24 20 R Arginine
24 26 40 D Aspartic acid
8 15 62 N Asparagine
5 9 13 M Methionine
13 20 29 K Lycine
18 26 49 V Valine
23 22 18 E Glutamic acid
10 16 12 H Histidine 

3UYY_1|Chains A, B|Branched-chain-amino-acid aminotransferase|Deinococcus radiodurans (1299)
>8AEM_1|Chain A|Casein kinase II subunit alpha|Homo sapiens (9606)
>1CXH_1|Chain A|CYCLODEXTRIN GLYCOSYLTRANSFERASE|Bacillus circulans (1397)
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 \(w=f(c)\)
3UYY , Knot 157 358 0.86 40 220 343 
MRLTILGMTAHDSRPEQAKKLADIDWSTLGFSYIRTDLRYLAHWKDGEWDAGTLTEDNQIHLAEGSTALHYGQQCFEGLKAYRCADGSINLFRPDQNAARMRMSCRRLLMPELSDEQFIDACLQVVRANEHFLPPYGTGGSLYLRPFVIGVGDNIGVRTAPEFIFSVFCVPVGPYFKGGLTPTNFITSDYDRAAPHGTGAAKVGGNYAASLLPGYEAKKRDFADVIYLDPATHTTIEEAGAANFFAITQDGQKFVTPQSPSILPSITKYSLLWLAEHRLGLEVEEGDIRIDELGKFSEAGACGTAAVITPIGGIQHGDDFHVFYSESEPGPVTRRLYDELVGIQYGDKEAPEGWIVKV
8AEM , Knot 147 328 0.86 40 194 315 
SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
1CXH , Knot 265 686 0.84 40 269 621 
APDTSVSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGTCTNLRLYCGGDWQGIINKINDGYLTGMGVTAIWISQPVENIYSIINYSGVNNTAYHGYWARDFKKTNPAYGTIADFQNLIAAAHAKNIKVIIDFAPNHTSPASSDQPSFAENGRLYDNGTLLGGYTNDTQNLFHHNGGTDFSTTENGIYKNLYDLADLNHNNSTVDVYLKDAIKMWLDLGIDGIRMDAVKHMPFGWQKSFMAAVNNYKPVFTFGEWFLGVNEVSPENHKFANESGMSLLDFRFAQKVRQVFRDNTDNMYGLKAMLEGSAADYAQVDDQVTFIDNHDMERFHASNANRRKLEQALAFTLTSRGVPAIYYGTEQYMSGGTDPDNRARIPSFSTSTTAYQVIQKLAPLRKCNPAIAYGSTQERWINNDVLIYERKFGSNVAVVAVNRNLNAPASISGLVTSLPQGSYNDVLGGLLNGNTLSVGSGGAASNFTLAAGGTAVWQYTAATATPTIGHVGPMMAKPGVTITIDGRGFGSSKGTVYFGTTAVSGADITSWEDTQIKVKIPAVAGGNYNIKVANAAGTASNVYDNFEVLSGDQVSVRFVVNNATTALGQNVYLTGSVSELGNWDPAKAIGPMYNQVVYQYPNWYYDVSVPAGKTIEFKFLKKQGSTVTWEGGSNHTFTAPSSGTATINVNWQP

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 \(c\).

\(|P_{f(3UYY_1)}(2) \setminus P_{f(8AEM_1)}(2)|=98\), \(|P_{f(8AEM_1)}(2) \setminus P_{f(3UYY_1)}(2)|=72\). 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 1:1010111101000010010011010100111001000100110100101011010000010110100110010001011010001010101101000110101000011110100001101010110100011110101101010111111100111001101110110111110101110100110000001110101110111001101111001000011011010110000100111101111000100110100101110100001111100011101001010100110100111010111101111100100101100000111100010001111001000110111101
Pair \(Z_2\) Length of longest common subsequence
3UYY_1,8AEM_1 170 4
3UYY_1,1CXH_1 159 4
8AEM_1,1CXH_1 177 4

Newick tree

 
[
	8AEM_1:89.05,
	[
		3UYY_1:79.5,1CXH_1:79.5
	]:9.55
]

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 \((0.85)(0.8)(\frac{686 }{\log_{20} 686}-\frac{328}{\log_{20}328})=98.6\)
Status Protein1 Protein2 d d1/2
Query variables 3UYY_1 8AEM_1 125 119.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]