CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7ONT_1 8DYZ_1 7WGR_1 Letter Amino acid
9 1 33 H Histidine
14 7 45 T Threonine
9 2 23 M Methionine
1 6 12 W Tryptophan
16 3 27 Y Tyrosine
21 6 64 V Valine
25 6 48 I Isoleucine
38 8 83 L Leucine
18 2 59 E Glutamic acid
10 3 44 F Phenylalanine
30 10 49 S Serine
11 11 54 R Arginine
2 8 18 C Cysteine
25 7 54 D Aspartic acid
14 3 41 Q Glutamine
24 12 54 G Glycine
33 6 45 K Lycine
16 2 50 P Proline
20 12 55 A Alanine
16 14 37 N Asparagine 

7ONT_1|Chains A, B|Poly [ADP-ribose] polymerase 1|Homo sapiens (9606)
>8DYZ_1|Chain A|Lysozyme C|Gallus gallus (9031)
>7WGR_1|Chains A, B|2-oxoglutarate dehydrogenase, mitochondrial|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 \(w=f(c)\)
7ONT , Knot 152 352 0.84 40 205 334 
GSKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
8DYZ , Knot 66 129 0.82 40 104 127 
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
7WGR , Knot 340 895 0.86 40 324 835 
AVQSLIRAYQIRGHHVAQLDPLGILDADLDSSVPADIISSTDKLGFYGLDESDLDKVFHLPTTTFIGGQESALPLREIIRRLEMAYCQHIGVEFMFINDLEQCQWIRQKFETPGIMQFTNEEKRTLLARLVRSTRFEEFLQRKWSSEKRFGLEGCEVLIPALKTIIDKSSENGVDYVIMGMPHRGRLNVLANVIRKELEQIFCQFDSKLEAADEGSGDVKYHLGMYHRRINRVTDRNITLSLVANPSHLEAADPVVMGKTKAEQFYCGDTEGKKVMSILLHGDAAFAGQGIVYETFHLSDLPSYTTHGTVHVVVNNQIGFTTDPRMARSSPYPTDVARVVNAPIFHVNSDDPEAVMYVCKVAAEWRSTFHKDVVVDLVCYRRNGHNEMDEPMFTQPLMYKQIRKQKPVLQKYAELLVSQGVVNQPEYEEEISKYDKICEEAFARSKDEKILHIKHWLDSPWPGFFTLDGQPRSMSCPSTGLTEDILTHIGNVASSVPVENFTIHGGLSRILKTRGEMVKNRTVDWALAEYMAFGSLLKEGIHIRLSGQDVERGTFSHRHHVLHDQNVDKRTCIPMNHLWPNQAPYTVCNSSLSEYGVLGFELGFAMASPNALVLWEAQFGDFHNTAQCIIDQFICPGQAKWVRQNGIVLLLPHGMEGMGPEHSSARPERFLQMCNDDPDVLPDLKEANFDINQLYDCNWVVVNCSTPGNFFHVLRRQILLPFRKPLIIFTPKSLLRHPEARSSFDEMLPGTHFQRVIPEDGPAAQNPENVKRLLFCTGKVYYDLTRERKARDMVGQVAITRIEQLSPFPFDLLLKEVQKYPNAELAWCQEEHKNQGYYDYVKPRLRTTISRAKPVWYAGRDPAAAPATGNKKTHLTELQRLLDTAFDLDVFKNFS

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 \(c\).

\(|P_{f(7ONT_1)}(2) \setminus P_{f(8DYZ_1)}(2)|=139\), \(|P_{f(8DYZ_1)}(2) \setminus P_{f(7ONT_1)}(2)|=38\). 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 1:1000011011001101110100100111000101001111010000101100110010011001000001101000100111001110011110010010101011001101011001101100000001101000010001011000000101100010000100001001011011010001000000110010000111010000011111001101111011101011101101101100010000000101111111101111010010010010011010001011100010101010101101111011001100001100001100110101001101010100
Pair \(Z_2\) Length of longest common subsequence
7ONT_1,8DYZ_1 177 3
7ONT_1,7WGR_1 173 4
8DYZ_1,7WGR_1 250 3

Newick tree

 
[
	8DYZ_1:11.64,
	[
		7ONT_1:86.5,7WGR_1:86.5
	]:28.14
]

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 \((0.85)(0.8)(\frac{481 }{\log_{20} 481}-\frac{129}{\log_{20}129})=104.\)
Status Protein1 Protein2 d d1/2
Query variables 7ONT_1 8DYZ_1 133 90.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]