CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4FMT_1 1YBC_1 3GLE_1 Letter Amino acid
3 0 3 H Histidine
21 0 13 L Leucine
45 2 13 A Alanine
5 0 18 N Asparagine
18 3 22 G Glycine
9 0 10 Q Glutamine
8 2 40 T Threonine
7 0 12 F Phenylalanine
15 0 32 V Valine
1 3 0 C Cysteine
6 0 33 K Lycine
5 0 3 M Methionine
11 0 10 I Isoleucine
14 0 11 P Proline
16 0 19 S Serine
3 0 1 W Tryptophan
1 0 14 Y Tyrosine
13 0 1 R Arginine
14 0 19 D Aspartic acid
13 0 21 E Glutamic acid 

4FMT_1|Chains A, B, C, D|ChpT protein|Caulobacter crescentus (190650)
>1YBC_1|Chains A, B|5'-D(*GP*CP*GP*TP*AP*(BOE)P*AP*CP*GP*C)-3')|
>3GLE_1|Chains A, B, C|Pilin|Streptococcus pyogenes serotype M1 (301447)
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 \(w=f(c)\)
4FMT , Knot 99 228 0.78 40 137 213 
GSHMTETVTETTAPASPEADVQGPDFAAMLAARLCHDFISPASAIVSGLDLLEDPSAQDMRDDAMNLIASSARKLADLLQFTRVAFGASASAENFDSRELEKLAQGVFAHVRPTLDWQIEPQAMNKPSSRAVLNIAQIAASALPAGGVATVKGVAADGRFSIIADAKGPRARLRPEVLAGLKGEPLAEGLGGPWVQAAYLNALVRAAGGQIAVEIGEDRASIAAWVPA
1YBC , Knot 6 10 0.46 8 6 8 
GCGTATACGC
3GLE , Knot 127 295 0.81 38 164 279 
GPGSATTVHGETVVNGAKLTVTKNLDLVNSNALIPNTDFTFKIEPDTTVNEDGNKFKGVALNTPMTKVTYTNSDKGGSNTKTAEFDFSEVTFEKPGVYYYKVTEEKIDKVPGVSYDTTSYTVQVHVLWNEEQQKPVATYIVGYKEGSKVPIQFKASLDSTTLTVKKKVSGTGGDRSKDFNFGLTLKANQYYKASEKVMIEKTTKGGQAPVQTEASIDQLYHFTLKDGESIKVTNLPVGVDYVVTEDDYKSEKYTTNVEVSPQDGAVKNIAGNSTEQETSTDKDMTITFTNKKVFE

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 \(c\).

\(|P_{f(4FMT_1)}(2) \setminus P_{f(1YBC_1)}(2)|=135\), \(|P_{f(1YBC_1)}(2) \setminus P_{f(4FMT_1)}(2)|=4\). 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 1:100100010000111010101011011111110100011011011101101100101001000110111001001101101001111101010010000100110111101010101010101100100011101101110111111110101111010101110101101010101111101011101111111011010111011110111011000101111111
Pair \(Z_2\) Length of longest common subsequence
4FMT_1,1YBC_1 139 2
4FMT_1,3GLE_1 149 4
1YBC_1,3GLE_1 164 2

Newick tree

 
[
	3GLE_1:81.07,
	[
		4FMT_1:69.5,1YBC_1:69.5
	]:11.57
]

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 \((0.85)(0.8)(\frac{238 }{\log_{20} 238}-\frac{10}{\log_{20}10})=79.7\)
Status Protein1 Protein2 d d1/2
Query variables 4FMT_1 1YBC_1 95 49
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]