CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1QAC_1 6YIW_1 3LVG_1 Letter Amino acid
6 14 39 K Lycine
3 3 27 F Phenylalanine
6 8 22 P Proline
6 17 37 V Valine
3 16 31 N Asparagine
5 6 30 D Aspartic acid
2 12 9 C Cysteine
5 15 25 I Isoleucine
8 10 23 T Threonine
9 10 34 Y Tyrosine
6 14 57 A Alanine
8 10 31 Q Glutamine
8 25 26 G Glycine
4 2 29 R Arginine
18 34 32 S Serine
2 4 9 W Tryptophan
1 2 20 M Methionine
4 4 56 E Glutamic acid
0 3 20 H Histidine
10 14 67 L Leucine 

1QAC_1|Chains A, B|IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN|Homo sapiens (9606)
>6YIW_1|Chain A|Cationic trypsin|Bos taurus (9913)
>3LVG_1|Chains A, B, C|Clathrin heavy chain 1|Bos taurus (9913)
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 \(w=f(c)\)
1QAC , Knot 59 114 0.81 38 92 110 
DIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNSKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCLQYYSTPYSFGQGTKLEIKR
6YIW , Knot 101 223 0.81 40 140 216 
IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN
3LVG , Knot 244 624 0.84 40 285 576 
MGSSHHHHHHSSGLVPRGSHMLKFDVNTSAVQVLIEHIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFKPLLLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLEKHELIEFRRIAAYLFKGNNRWKQSVELCKKDSLYKDAMQYASESKDTELAEELLQWFLQEEKRECFGACLFTCYDLLRPDVVLETAWRHNIMDFAMPYFIQVMKEYLTKVDKLDASESLRKEEEQATETQPIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGYSM

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 \(c\).

\(|P_{f(1QAC_1)}(2) \setminus P_{f(6YIW_1)}(2)|=44\), \(|P_{f(6YIW_1)}(2) \setminus P_{f(1QAC_1)}(2)|=92\). 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 1:011100010011101100101000000011000000001110000110110111011000001110010101010010101001010011100010000010011010010100
Pair \(Z_2\) Length of longest common subsequence
1QAC_1,6YIW_1 136 3
1QAC_1,3LVG_1 223 3
6YIW_1,3LVG_1 207 3

Newick tree

 
[
	3LVG_1:11.84,
	[
		1QAC_1:68,6YIW_1:68
	]:49.84
]

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 \((0.85)(0.8)(\frac{337 }{\log_{20} 337}-\frac{114}{\log_{20}114})=68.9\)
Status Protein1 Protein2 d d1/2
Query variables 1QAC_1 6YIW_1 85 64
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]