CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5ZUF_1 7PAA_1 9CAG_1 Letter Amino acid
2 4 14 C Cysteine
14 9 42 E Glutamic acid
18 35 40 G Glycine
13 5 27 F Phenylalanine
27 32 36 S Serine
4 5 7 W Tryptophan
27 13 41 A Alanine
16 14 32 R Arginine
14 8 20 N Asparagine
11 9 27 I Isoleucine
25 20 41 T Threonine
14 12 34 D Aspartic acid
12 9 41 K Lycine
12 15 19 Y Tyrosine
11 9 26 Q Glutamine
5 4 18 H Histidine
18 12 57 L Leucine
11 4 18 M Methionine
23 12 30 P Proline
20 21 42 V Valine 

5ZUF_1|Chain A|Capsid protein VP1|Enterovirus A71 (39054)
>7PAA_1|Chains A[auth KKK], L[auth WWW], M[auth XXX], N[auth YYY], O[auth ZZZ], P[auth aaa], Q[auth bbb], R[auth ccc], S[auth ddd], T[auth eee]|scFv 29B1|Homo sapiens (9606)
>9CAG_1|Chain A|DNA topoisomerase 3-beta-1|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 \(w=f(c)\)
5ZUF , Knot 133 297 0.85 40 191 285 
GDRVADVIESSIEDSSSRALTHALPAPTGQNTQVSSHRLDTGKVPALQAAEIGASSNASDESMIETRCVLNSHSTAETTLDSFFSRAGLVGEIDLPLKGTTNPNGYANWDIDITGYAQMRRKVELFTYMRFDAEFTFVACTPTGEVVPQLLQYMFVPPGAPKPDSRESLAWQTATNPSVFVKLSDPPAQVSVPFMSPASAYQWFYDGYPTFGEHKQEKDLEYGAMPNNMMGTFSVRTVGTSKSKYPLVVRIYMRMKHVRAWIPRPMRNQNYLFKANPNYAGNSIKPTGASRTAITTL
7PAA , Knot 109 252 0.79 40 154 234 
GSYVLTQPPSVSVAPGKTARITCGGNNIGSRSVHWYQHKPGQAPVMIISYDMNRPSGIPERVSGSNYGNTATLTISRVEAGDEADYYCQVWDSRSDHPYVFGTGTRVTVLGSTSGSGKPGSGEGSTKGEVQLVESGGGLVKPGGSLRLSCAASGITFQYYAMNWVRQAPGKGLEWVSSIGGRGDTTYYTDSVKGRFTISRDNSKSTLYLQMNSLRAEDTAVYYCAKEPFDSSGDHRGVFDYWGQGTLVTVSS
9CAG , Knot 241 612 0.84 40 282 577 
VMKTVLMVAEKPSLAQSIAKILSRGSLSSHKGLNGACSVHEYTGTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNKAHGGEKTVFRARFSSITDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGDLDSSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNTDKDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQGYISFPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAEGINRPRKGHDAGDHPPITPMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSIAGMDELMEVSF

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 \(c\).

\(|P_{f(5ZUF_1)}(2) \setminus P_{f(7PAA_1)}(2)|=101\), \(|P_{f(7PAA_1)}(2) \setminus P_{f(5ZUF_1)}(2)|=64\). 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 1:100110110001000000110011111010000100001001011110110111000100001100001100000100010011001111101011101000101010101010101010001011001010101011100101011101100111111110100000111001001011101001110101111011010011001010110000000100111100111010100110000001111010101001011110110000011010100110010101100011001
Pair \(Z_2\) Length of longest common subsequence
5ZUF_1,7PAA_1 165 3
5ZUF_1,9CAG_1 177 4
7PAA_1,9CAG_1 188 4

Newick tree

 
[
	9CAG_1:94.03,
	[
		5ZUF_1:82.5,7PAA_1:82.5
	]:11.53
]

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 \((0.85)(0.8)(\frac{549 }{\log_{20} 549}-\frac{252}{\log_{20}252})=84.4\)
Status Protein1 Protein2 d d1/2
Query variables 5ZUF_1 7PAA_1 109 98.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]