CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8PCW_1 9EJG_1 3VIU_1 Letter Amino acid
23 7 70 A Alanine
4 0 13 M Methionine
14 7 18 Y Tyrosine
26 10 13 N Asparagine
30 10 21 D Aspartic acid
38 8 20 I Isoleucine
12 11 45 P Proline
27 18 31 S Serine
13 11 29 T Threonine
0 4 6 W Tryptophan
15 6 12 Q Glutamine
31 13 86 E Glutamic acid
11 9 81 G Glycine
10 7 13 H Histidine
40 19 97 L Leucine
37 9 28 K Lycine
19 17 65 V Valine
17 4 57 R Arginine
2 3 4 C Cysteine
21 10 16 F Phenylalanine

8PCW_1|Chains A, B|CRISPR system endoribonuclease Csm6'|Streptococcus thermophilus (1308)
>9EJG_1|Chain A|HLA class II histocompatibility antigen, DQ alpha 1 chain|Homo sapiens (9606)
>3VIU_1|Chain A|Phosphoribosylformylglycinamidine synthase 2|Thermus thermophilus (300852)
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 \(w=f(c)\)
8PCW , Knot 163 390 0.83 38 203 365
GANAMGVLISAVGDTDPFRNFHDGALIHIARKYRPEKVILIFSEHTAKKQGNIEKALFSIAPNYEPELIIHDPIISDNEVHIFDVMFQRFSDILQEYYTKEDEFILNLSSATPQIKSALFVINRLNGINVKAVQVSSPEHASNENIGHDNDENIDELIEVNKDNKVNFIDRTIEDNAEKFSQALLKKTARDFIEKFDYKAALDILDQLSDFPNLKSVREEIRDVVNCLSKQDVPKGLRHKKLKEEEQKILSAYLTIELQRERGNVSESFIRIKNLTEFILEDYIKKRYPGLIDEYCEDIQKYYLSLFDYSKLLKATKEFKLKRTIAPIIDMNSSRNKVAHSLSPLDSDAVKQLGIAMKTLKTLVREQYHFSQSDFNFYQDLNKILLTKLN
9EJG , Knot 86 183 0.81 38 137 178
EDIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPE
3VIU , Knot 261 725 0.79 40 240 595
MEALAKEIGIPEGEYREIVQRLGREPNRVELLLFKVMWSEHCAYKNSRPLLKALPKEGEAVLQGPGENAGVVRVGEGWAVAFKIESHNHPSAVEPFQGAATGVGGILRDIMSMGARPIALLDSLRFGPPEEARSRYLLKGVVSGIAFYGNAIGVPTVGGDLYFHEGYRENPLVNAMCLGLLREEHLKRSRASLGRPIYYAGAKTGRDGIGGAAFASRELKEEKAEDRPAVQVGDPFLGKLLMEATLEAIELDLVEGVQDMGAAGLTSSLSELAHKSGLGVELHLDLVPTREEGMTPEELLLSESQERMVLVPKEGKEKALEEVFGRWGLDCVPVARTIPERVFRVLFRGEVVAEVPTEALAEAPTYVRVGREDPEVRRLRETPIPPLEADPQEVLRRLLASPNLASREAVYERYDHQVGTRTALLPGKGDAAVLWIKGTRLGVAAKVDQNPRYSRLHPRLGAMHALAEACRNVSVVGAKPLAYTDGLNLGSPETPEGYHELAETIAGLKEASEALGVPVVSGNVSLYNESGGKRIPPTAMVGVVGVLEVDKRAEMGFRRPGEVLLLIGEERGELGASEVLYLLTGKEFGHPPRLDLGREKAVQEAIRDLIQRGLTRTAHDVAEGGLLLALAEMTFPYGVGATVEVREEGLEALFGEAPSRVLFTVEKTRLQEATLLLEERGLPYRVLGETGGKSLTVLTPGGVLEWSLEELLSAWKAPLREVLDG

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 \(c\).

\(|P_{f(8PCW_1)}(2) \setminus P_{f(9EJG_1)}(2)|=117\), \(|P_{f(9EJG_1)}(2) \setminus P_{f(8PCW_1)}(2)|=51\). 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 1:110111111011100011001001111011000010011111000010001010011101110001011100111000010110111001001100000000011101001010100111110010110101101001001000011000000100110100000101100010001001001110001001100100011101100100110100100010011001000011011000010000001101010101000010100011010010011100010000111100000010000101100001101000101000111110100000011001011000110011111001001100000100001010001001110010
Pair \(Z_2\) Length of longest common subsequence
8PCW_1,9EJG_1 168 3
8PCW_1,3VIU_1 155 4
9EJG_1,3VIU_1 181 4

Newick tree

 
[
	9EJG_1:90.34,
	[
		8PCW_1:77.5,3VIU_1:77.5
	]:12.84
]

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 \((0.85)(0.8)(\frac{573 }{\log_{20} 573}-\frac{183}{\log_{20}183})=112.\)
Status Protein1 Protein2 d d1/2
Query variables 8PCW_1 9EJG_1 142 104
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]