CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1NIO_1 8INL_1 8ZNI_1 Letter Amino acid
22 73 60 L Leucine
19 41 49 K Lycine
3 12 17 M Methionine
11 27 28 F Phenylalanine
27 40 80 S Serine
27 55 43 A Alanine
18 27 44 N Asparagine
10 43 53 E Glutamic acid
11 17 38 Y Tyrosine
21 31 49 I Isoleucine
9 37 86 P Proline
11 47 93 G Glycine
1 16 31 H Histidine
1 9 16 W Tryptophan
16 53 64 V Valine
9 32 38 R Arginine
0 9 60 C Cysteine
10 37 39 Q Glutamine
8 30 30 D Aspartic acid
13 33 59 T Threonine 

1NIO_1|Chain A|b-luffin|Luffa aegyptiaca (3670)
>8INL_1|Chain A|Lysine-specific histone demethylase 1A|Homo sapiens (9606)
>8ZNI_1|Chain A|Complement receptor type 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 \(w=f(c)\)
1NIO , Knot 107 247 0.79 38 148 231 
ANVSFSLSGADSKSYSKFITALRKALPSKEKVSNIPLLLPSASGASRYILMQLSNYDAKAITMAIDVTNVYIMGYLVNSTSYFFNESDAKLASQYVFKGSTIVTLPYSGNYERLQNAAGKVREKIPLGFRAFDSAITSLFHYDSTAAAGAFLVIIQTTAEASRFKYIEGQIIKRIPKNEVPSPAALSLENEWSALSKQIQLAQTNNGAFRTPVVIIDNKGQRVEIKDVNSKVVTNNIKLLLNKQNIA
8INL , Knot 261 669 0.84 40 279 617 
GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
8ZNI , Knot 349 977 0.82 40 314 817 
MGAAGLLGVFLALVAPGVLGISCGSPPPILNGRISYYSTPIAVGTVIRYSCSGTFRLIGEKSLLCITKDKVDGTWDKPAPKCEYFNKYSSCPEPIVPGGYKIRGSTPYRHGDSVTFACKTNFSMNGNKSVWCQANNMWGPTRLPTCVSVFPLECPALPMIHNGHHTSENVGSIAPGLSVTYSCESGYLLVGEKIINCLSSGKWSAVPPTCEEARCKSLGRFPNGKVKEPPILRVGVTANFFCDEGYRLQGPPSSRCVIAGQGVAWTKMPVCEEIFCPSPPPILNGRHIGNSLANVSYGSIVTYTCDPDPEEGVNFILIGESTLRCTVDSQKTGTWSGPAPRCELSTSAVQCPHPQILRGRMVSGQKDRYTYNDTVIFACMFGFTLKGSKQIRCNAQGTWEPSAPVCEKECQAPPNILNGQKEDRHMVRFDPGTSIKYSCNPGYVLVGEESIQCTSEGVWTPPVPQCKVAACEATGRQLLTKPQHQFVRPDVNSSCGEGYKLSGSVYQECQGTIPWFMEIRLCKEITCPPPPVIYNGAHTGSSLEDFPYGTTVTYTCNPGPERGVEFSLIGESTIRCTSNDQERGTWSGPAPLCKLSLLAVQCSHVHIANGYKISGKEAPYFYNDTVTFKCYSGFTLKGSSQIRCKADNTWDPEIPVCEKETCQHVRQSLQELPAGSRVELVNTSCQDGYQLTGHAYQMCQDAENGIWFKKIPLCKVIHCHPPPVIVNGKHTGMMAENFLYGNEVSYECDQGFYLLGEKKLQCRSDSKGHGSWSGPSPQCLRSPPVTRCPNPEVKHGYKLNKTHSAYSHNDIVYVDCNPGFIMNGSRVIRCHTDNTWVPGVPTCIKKAFIGCPPPPKTPNGNHTGGNIARFSPGMSILYSCDQGYLLVGEALLLCTHEGTWSQPAPHCKEVNCSSPADMDGIQKGLEPRKMYQYGAVVTLECEDGYMLEGSPQSQCQSDHQWNPPLAVCRSRHHHHHH

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 \(c\).

\(|P_{f(1NIO_1)}(2) \setminus P_{f(8INL_1)}(2)|=22\), \(|P_{f(8INL_1)}(2) \setminus P_{f(1NIO_1)}(2)|=153\). 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 1:1010101011000000011011001110000100111111010110001110100001011011101001011101100000110000101100011010011011001000010011101000111110110011001100000111111111100010100100101011001100011011110100010110001011000011100111110001001010010001100010111000011
Pair \(Z_2\) Length of longest common subsequence
1NIO_1,8INL_1 175 4
1NIO_1,8ZNI_1 216 4
8INL_1,8ZNI_1 137 5

Newick tree

 
[
	1NIO_1:10.37,
	[
		8INL_1:68.5,8ZNI_1:68.5
	]:37.87
]

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 \((0.85)(0.8)(\frac{916 }{\log_{20} 916}-\frac{247}{\log_{20}247})=182.\)
Status Protein1 Protein2 d d1/2
Query variables 1NIO_1 8INL_1 235 158
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]