CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8DLN_1 3HHC_1 8UVA_1 Letter Amino acid
12 2 3 W Tryptophan
58 11 40 D Aspartic acid
26 7 28 H Histidine
58 8 18 K Lycine
95 12 33 T Threonine
78 21 53 A Alanine
41 17 39 R Arginine
11 3 7 M Methionine
54 0 16 Y Tyrosine
96 13 54 V Valine
88 2 12 N Asparagine
66 10 17 Q Glutamine
79 5 17 F Phenylalanine
67 13 42 P Proline
106 34 53 L Leucine
105 8 30 S Serine
30 8 6 C Cysteine
50 10 40 E Glutamic acid
96 9 53 G Glycine
72 3 31 I Isoleucine 

8DLN_1|Chain A[auth B]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049)
>3HHC_1|Chains A, B, C, D|Interleukin-28B|Homo sapiens (9606)
>8UVA_1|Chains A, B, C, D|CTP synthase|Mycobacterium tuberculosis (1773)
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 \(w=f(c)\)
8DLN , Knot 454 1288 0.84 40 328 1103 
MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLLALHISYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGVENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK
3HHC , Knot 91 196 0.81 38 124 188 
MTGDCMPVLVLMAAVLTVTGAVPVARLRGALPDARGCHIAQFKSLSPQELQAFKRAKDALEESLLLKDCKCRSRLFPRTWDLRQLQVRERPVALEAELALTLKVLEATADTDPALGDVLDQPLHTLHHILSQLRACIQPQPTAGPRTRGRLHHWLHRLQEAPKKESPGCLEASVTFNLFRLLTRDLNCVASGDLCV
8UVA , Knot 230 592 0.82 40 245 540 
MRKHPQTATKHLFVSGGVASSLGKGLTASSLGQLLTARGLHVTMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDVGHYERFLDRNLPGSANVTTGQVYSTVIAKERRGEYLGDTVQVIPHITDEIKRRILAMAQPDADGNRPDVVITEIGGTVGDIESQPFLEAARQVRHYLGREDVFFLHVSLVPYLAPSGELKTKPTQHSVAALRSIGITPDALILRCDRDVPEALKNKIALMCDVDIDGVISTPDAPSIYDIPKVLHREELDAFVVRRLNLPFRDVDWTEWDDLLRRVHEPHETVRIALVGKYVELSDAYLSVAEALRAGGFKHRAKVEICWVASDGCETTSGAAAALGDVHGVLIPGGFGIRGIEGKIGAIAYARARGLPVLGLCLGLQCIVIEAARSVGLTNANSAEFDPDTPDPVIATMPDQEEIVAGEADLGGTMRLGSYPAVLEPDSVVAQAYQTTQVSERHRHRYEVNNAYRDKIAESGLRFSGTSPDGHLVEFVEYPPDRHPFVVGTQAHPELKSRPTRPHPLFVAFVGAAIDYKAGELLPVEIPEIPEHTPNGSSHRDGVGQPLPEPASRGHHHHHH

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 \(c\).

\(|P_{f(8DLN_1)}(2) \setminus P_{f(3HHC_1)}(2)|=215\), \(|P_{f(3HHC_1)}(2) \setminus P_{f(8DLN_1)}(2)|=11\). 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 1:1111111111100001010000011110000100110010011000110000011111100101101101010010001101111100110110000001101111100100000011110010011101001010001111100000000110001010001000010010011110101001010010011100101010100000110110111011011011101111101001001111010010110000110111110011010100111000001010011001101100000010010100110000010101000110110100101110110100110101100001000110001100010100100011010010010100101001110100100111100101100000110010101111000010001110000100110000101100010001001100100110110001110001101001110010011110101101110101100000110000101010110101110000001111001100110000110010010110101001111011011000000111100110000111110100101010100010011000110111100100000001111111010000000011010011000111001011100011000001111001010100011110100001000101010000000111001010001001101111000000001110100100011100111101001110100100001100111001011011110001001101110011010010110111111000111000011111010011011111110111110110010111100011000001110010011101000100010111010011000101100110010001111001100110010110101010011010100100010001101101010101110010001110000101010100110110011011111010011100001001111000101011001111001001110000100101100000110100011111100010011010100100010001000001010110101101011010001001001100100011010011000010101101100101010001011110011100101110111000000000110010100111011110110110010100
Pair \(Z_2\) Length of longest common subsequence
8DLN_1,3HHC_1 226 4
8DLN_1,8UVA_1 127 7
3HHC_1,8UVA_1 169 5

Newick tree

 
[
	3HHC_1:10.21,
	[
		8DLN_1:63.5,8UVA_1:63.5
	]:45.71
]

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 \((0.85)(0.8)(\frac{1484 }{\log_{20} 1484}-\frac{196}{\log_{20}196})=338.\)
Status Protein1 Protein2 d d1/2
Query variables 8DLN_1 3HHC_1 425 242.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]