CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7YZM_1 5VZX_1 4BKR_1 Letter Amino acid
33 12 26 K Lycine
22 12 16 P Proline
14 19 22 T Threonine
35 21 30 V Valine
24 5 13 R Arginine
8 3 8 H Histidine
40 17 33 L Leucine
27 3 26 I Isoleucine
30 14 37 A Alanine
21 7 30 D Aspartic acid
13 7 21 Q Glutamine
10 36 22 S Serine
4 3 5 W Tryptophan
18 9 14 N Asparagine
7 2 8 M Methionine
19 6 14 F Phenylalanine
13 10 14 Y Tyrosine
11 5 5 C Cysteine
44 6 22 E Glutamic acid
29 23 40 G Glycine 

7YZM_1|Chains A, B, E[auth C], F[auth D]|Dehydratase family protein|Carboxydothermus hydrogenoformans Z-2901 (246194)
>5VZX_1|Chains A[auth E], C[auth H]|Crenezumab Fab heavy chain|Homo sapiens (9606)
>4BKR_1|Chain A|PUTATIVE REDUCTASE YPZ3_3519|YERSINIA PESTIS (1035377)
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 \(w=f(c)\)
7YZM , Knot 174 422 0.83 40 219 402 
GMDNRELWKVLNVDLEKHDEFLAPVPAVYRELFLNRPNRPRAMAYFDAVVGDIHGIRVHELYNLKQEGKKVFATFCVYVPEEIINATGSACIGLCGGAQYTVPAGETVLPRNLCPLIKSAMGFKIERICPYFQVADYVVGETTCDGKKKAWEILNEYIPVYVMELPQKKEERDRKFWEEEIKDFAQFVEEKTGVKLNAENLRAGIEKINKKRKALKRLSDLRKHNPAPIHGLDVLLINQLAFFDDPERFATKVNELCDELEERVAKGEGVVSKDAPRILITGTPQPIPHWKIHALIEGAGGVVVGEETCIGERYFKDLVEPAADVEGMLKNIAARSLKVNCACFTPNTGRLEDILSMVQKLQVDGVIHYSLQFCQPYGVESYLVGRELERRNIPFLKLESDFSEEDQGQLKTRIEAFLEMIK
5VZX , Knot 95 220 0.77 40 138 208 
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYGMSWVRQAPGKGLELVASINSNGGSTYYPDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCASGDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
4BKR , Knot 170 406 0.83 40 232 391 
RGSHMLEMIIKPRVRGFICVTAHPTGCEANVKKQIDYVTTEGPIANGPKRVLVIGASTGYGLAARITAAFGCGADTLGVFFERPGEEGKPGTSGWYNSAAFHKFAAQKGLYAKSINGDAFSDEIKQLTIDAIKQDLGQVDQVIYSLASPRRTHPKTGEVFNSALKPIGNAVNLRGLDTDKEVIKESVLQPATQSEIDSTVAVMGGEDWQMWIDALLDAGVLAEGAQTTAFTYLGEKITHDIYWNGSIGAAKKDLDQKVLAIRESLAAHGGGDARVSVLKAVVTQASSAIPMMPLYLSLLFKVMKEKGTHEGCIEQVYSLYKDSLCGDSPHMDQEGRLRADYKELDPEVQNQVQQLWDQVTNDNIYQLTDFVGYKSEFLNLFGFGIDGVDYDADVNPDVKIPNLIQG

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 \(c\).

\(|P_{f(7YZM_1)}(2) \setminus P_{f(5VZX_1)}(2)|=135\), \(|P_{f(5VZX_1)}(2) \setminus P_{f(7YZM_1)}(2)|=54\). 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 1:11000011011010100000111111110001110010010111010111101011010010010001001110101011001101010101110111000111100111001011100111101001010101100111000001000110110001110110110000000001100010011011000011010100101110010000011001001000011110110111100111100100110010010001000110101110001101110101011101010111011111111000011000100110111010111001110010100101010010100110110010101110001010010110001110010000111101000100000101000101110110
Pair \(Z_2\) Length of longest common subsequence
7YZM_1,5VZX_1 189 3
7YZM_1,4BKR_1 149 4
5VZX_1,4BKR_1 170 3

Newick tree

 
[
	5VZX_1:94.44,
	[
		7YZM_1:74.5,4BKR_1:74.5
	]:19.94
]

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 \((0.85)(0.8)(\frac{642 }{\log_{20} 642}-\frac{220}{\log_{20}220})=119.\)
Status Protein1 Protein2 d d1/2
Query variables 7YZM_1 5VZX_1 152 115
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]