CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4UQC_1 1WVO_1 7GLE_1 Letter Amino acid
11 0 3 W Tryptophan
2 0 12 C Cysteine
15 0 14 Q Glutamine
21 7 9 E Glutamic acid
27 10 26 G Glycine
22 5 29 L Leucine
15 3 10 M Methionine
21 5 13 P Proline
20 1 11 Y Tyrosine
18 5 17 D Aspartic acid
32 10 27 V Valine
32 2 21 N Asparagine
25 5 24 T Threonine
29 1 17 A Alanine
22 0 11 R Arginine
15 1 7 H Histidine
18 5 11 I Isoleucine
20 9 11 K Lycine
13 1 17 F Phenylalanine
31 9 16 S Serine 

4UQC_1|Chain A|CARBOHYDRATE BINDING FAMILY 6|RUMINICLOSTRIDIUM THERMOCELLUM (1515)
>1WVO_1|Chain A|Sialic acid synthase|Homo sapiens (9606)
>7GLE_1|Chains A, B|3C-like proteinase|Severe acute respiratory syndrome coronavirus 2 (2697049)
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 \(w=f(c)\)
4UQC , Knot 174 409 0.85 40 240 391 
MGSSHHHHHHSSGLVPRGSHMASATINLSAEKQVIRGFGGMNHPVWISDLTPQQRDTAFGNGEGQLGFTILRIHVDENRNNWSKEVATARRAIELGAIVSASPWNPPSNMVETFTRNGVPNQKRLRYDKYGDYVQHLNDFVAYMKSNGVDLYAISVQNEPDYAHEWTWWTPQEMLRFMRDYAGQINCRVMAPESFQYLKNMSDPILNDPQALANLDILGAHFYGTTVNNMPYPLFEQKGAGKELWMTEVYVPNSDSNSADRWPEALEVAHNMHNALVEGNFQAYVWWYIRRSYGPMKEDGTISKRGYMMAHYSKFVRPGYVRVDATKNPTYNVYLSACKNKKDNSVVAVVINKSTEAKTINISVPGTSIRKWERYVTTGSKNLRKESDINASGTTFQVTLEPQSVTTFV
1WVO , Knot 38 79 0.70 32 55 71 
GSSGSSGSVVAKVKIPEGTILTMDMLTVKVGEPKGYPPEDIFNLVGKKVLVTVEEDDTIMEELVDNHGKKIKSSGPSSG
7GLE , Knot 134 306 0.83 40 196 290 
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

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 \(c\).

\(|P_{f(4UQC_1)}(2) \setminus P_{f(1WVO_1)}(2)|=203\), \(|P_{f(1WVO_1)}(2) \setminus P_{f(4UQC_1)}(2)|=18\). 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 1:1100000000001111010011010101010001101111100111100101000001110101011101101010000001000110100110111110101101100110010001110000100000100100100111010001101011010001001001011010011011000110100011110010010010011100101110101111010100100110111000111001110010110000001001101101100100111010101011101000011100010100010111000011011010101000100010101000000001111110000010010101110010010001001000100000101010010101010010011
Pair \(Z_2\) Length of longest common subsequence
4UQC_1,1WVO_1 221 4
4UQC_1,7GLE_1 190 4
1WVO_1,7GLE_1 177 4

Newick tree

 
[
	4UQC_1:10.45,
	[
		7GLE_1:88.5,1WVO_1:88.5
	]:18.95
]

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 \((0.85)(0.8)(\frac{488 }{\log_{20} 488}-\frac{79}{\log_{20}79})=123.\)
Status Protein1 Protein2 d d1/2
Query variables 4UQC_1 1WVO_1 161 94.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]