CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2BUA_1 9BLU_1 8IOV_1 Letter Amino acid
55 8 28 Y Tyrosine
44 47 31 V Valine
31 21 18 R Arginine
11 4 8 C Cysteine
45 34 22 I Isoleucine
52 38 60 L Leucine
36 36 35 K Lycine
65 26 35 S Serine
38 21 39 N Asparagine
41 34 33 D Aspartic acid
31 27 31 Q Glutamine
12 12 21 M Methionine
36 49 38 A Alanine
42 30 47 E Glutamic acid
33 16 27 F Phenylalanine
48 37 33 T Threonine
20 2 20 W Tryptophan
40 47 33 G Glycine
20 5 22 H Histidine
28 20 27 P Proline 

2BUA_1|Chains A, B, C, D|DIPEPTIDYL PEPTIDASE IV|SUS SCROFA (9823)
>9BLU_1|Chain A|Stress-70 protein, mitochondrial|Homo sapiens (9606)
>8IOV_1|Chain A|Processed angiotensin-converting enzyme 2|Homo sapiens (9606)
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 \(w=f(c)\)
2BUA , Knot 281 728 0.84 40 308 670 
SRRTYTLTDYLKSTFRVKFYTLQWISDHEYLYKQENNILLFNAEYGNSSIFLENSTFDELGYSTNDYSVSPDRQFILFEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWITWSPVGHKLAYVWNNDIYVKNEPNLSSQRITWTGKENVIYNGVTDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRIPYPKAGAENPTVKFFVVDTRTLSPNASVTSYQIVPPASVLIGDHYLCGVTWVTEERISLQWIRRAQNYSIIDICDYDESTGRWISSVARQHIEISTTGWVGRFRPAEPHFTSDGNSFYKIISNEEGYKHICHFQTDKSNCTFITKGAWEVIGIEALTSDYLYYISNEHKGMPGGRNLYRIQLNDYTKVTCLSCELNPERCQYYSASFSNKAKYYQLRCFGPGLPLYTLHSSSSDKELRVLEDNSALDKMLQDVQMPSKKLDVINLHGTKFWYQMILPPHFDKSKKYPLLIEVYAGPCSQKVDTVFRLSWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEATRQFSKMGFVDDKRIAIWGWSYGGYVTSMVLGAGSGVFKCGIAVAPVSKWEYYDSVYTERYMGLPTPEDNLDYYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQLSKALVDAGVDFQTMWYTDEDHGIASNMAHQHIYTHMSHFLKQCFSLP
9BLU , Knot 207 514 0.83 40 237 490 
MASEAIKGAVVGIDLGTTNSCVAVMEGKQAKVLENAEGARTTPSVVAFTADGERLVGMPAKRQAVTNPNNTFYATKRLIGWRYDDPEVQKDIKNVPFKIVRASNGDAWVEAHGKLYSPSQIGAFVLMKMKETAENYLGHTAKNAVITVPAYFNDSQRQATKDAGQISGLNVLRVINEPTAAALAYGLDKSEDKVIAVYDLGGGTFDISILEIQKGVFEVKSTNGDTFLGGEDFDQALLRHIVKEFKRETGVDLTKDNMALQRVREAAEKAKCELSSSVQTDINLPYLTMDSSGPKHLNMKLTRAQFEGIVTDLIRRTIAPCQKAMQDAEVSKSDIGEVILVGGMTRMPKVQQTVQDLFGRAPSKAVNPDEAVAIGAAIQGGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKKSQVFSTAADGQTQVEIKVCQGEREMAGDNKLLGQFTLIGIPPAPRGVPQIEVTFDIDANGIVHVSAKDKGTGREQQIVIQSSGGLSKDDIE
8IOV , Knot 249 608 0.87 40 290 578 
STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSGTKHHHHHH

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 \(c\).

\(|P_{f(2BUA_1)}(2) \setminus P_{f(9BLU_1)}(2)|=106\), \(|P_{f(9BLU_1)}(2) \setminus P_{f(2BUA_1)}(2)|=35\). 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 1:00000010001000101010010110000010000001111010010001110000100110000000101000111100001001000001000100100001100001100001101011100110110001010001010000101010001100110011000011010011110101011101010000111100010000010010010110101110010101111000010101010000111110111100010110110000101011001000011010000000101100110001010001111010110101000100100110000100010010000000011001110111101100001001000001111100100101000001001000101000000010100010000100111111100100000000101100001100110010110001011010100110011111010000001111010111000010011010110011000011110101010100100110110001101010001010001001111000011111100110100111111011100111111100100000100000111101000100000001100100100100111010100010100010100111011101001100000011100110001000100110001011
Pair \(Z_2\) Length of longest common subsequence
2BUA_1,9BLU_1 141 4
2BUA_1,8IOV_1 120 4
9BLU_1,8IOV_1 145 4

Newick tree

 
[
	9BLU_1:74.95,
	[
		2BUA_1:60,8IOV_1:60
	]:14.95
]

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 \((0.85)(0.8)(\frac{1242 }{\log_{20} 1242}-\frac{514}{\log_{20}514})=187.\)
Status Protein1 Protein2 d d1/2
Query variables 2BUA_1 9BLU_1 240 203
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]