CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5TJL_1 8ADH_1 1FKN_1 Letter Amino acid
29 25 29 L Leucine
13 30 15 K Lycine
17 20 19 P Proline
6 2 7 W Tryptophan
17 28 24 A Alanine
15 8 16 Q Glutamine
10 7 7 H Histidine
11 26 30 S Serine
16 24 23 T Threonine
13 4 19 Y Tyrosine
14 17 21 D Aspartic acid
17 38 34 G Glycine
18 18 20 F Phenylalanine
31 39 34 V Valine
7 8 15 N Asparagine
10 24 23 I Isoleucine
9 9 8 M Methionine
22 12 19 R Arginine
4 14 6 C Cysteine
18 21 22 E Glutamic acid 

5TJL_1|Chain A|Histo-blood group ABO system transferase|Homo sapiens (9606)
>8ADH_1|Chain A|APO-LIVER ALCOHOL DEHYDROGENASE|Equus caballus (9796)
>1FKN_1|Chains A, B|MEMAPSIN 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 \(w=f(c)\)
5TJL , Knot 134 297 0.85 40 196 289 
AIGEFMVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVRAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPGFYGSSREAFTYERRPQSQAYIPKDEGDFYYLGGFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPKNHQAVRNP
8ADH , Knot 158 374 0.83 40 210 358 
STAGKVIKCKAAVLWEEKKPFSIEEVEVAPPKAHEVRIKMVATGICRSDDHVVSGTLVTPLPVIAGHEAAGIVESIGEGVTTVRPGDKVIPLFTPQCGKCRVCKHPEGNFCLKNDLSMPRGTMQDGTSRFTCRGKPIHHFLGTSTFSQYTVVDEISVAKIDAASPLEKVCLIGCGFSTGYGSAVKVAKVTQGSTCAVFGLGGVGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATECVNPQDYKKPIQEVLTEMSNGGVDFSFEVIGRLDTMVTALSCCQEAYGVSVIVGVPPDSQNLSMNPMLLLSGRTWKGAIFGGFKSKDSVPKLVADFMAKKFALDPLITHVLPFEKINEGFDLLRSGESIRTILTF
1FKN , Knot 166 391 0.84 40 226 375 
RRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN

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 \(c\).

\(|P_{f(5TJL_1)}(2) \setminus P_{f(8ADH_1)}(2)|=83\), \(|P_{f(8ADH_1)}(2) \setminus P_{f(5TJL_1)}(2)|=97\). 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 1:111011101101101010110100001111011111111010101011000101000011101111000111101110010001111001000110001111101011010010110101000100101001011001000011001001101010101000111011011110101110100001100000100010110001010011111110100100100100011110010110111000001000110001001101001100011111111001010111000011001
Pair \(Z_2\) Length of longest common subsequence
5TJL_1,8ADH_1 180 3
5TJL_1,1FKN_1 168 4
8ADH_1,1FKN_1 162 3

Newick tree

 
[
	5TJL_1:88.97,
	[
		1FKN_1:81,8ADH_1:81
	]:7.97
]

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 \((0.85)(0.8)(\frac{671 }{\log_{20} 671}-\frac{297}{\log_{20}297})=103.\)
Status Protein1 Protein2 d d1/2
Query variables 5TJL_1 8ADH_1 132 119.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]