CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5LDP_1 7LYS_1 1RHR_1 Letter Amino acid
3 20 3 Y Tyrosine
20 72 3 A Alanine
5 36 11 D Aspartic acid
1 15 5 C Cysteine
11 42 12 G Glycine
5 18 3 H Histidine
3 7 4 M Methionine
5 13 0 W Tryptophan
10 50 10 T Threonine
4 26 10 N Asparagine
8 33 11 I Isoleucine
21 58 12 L Leucine
4 60 11 K Lycine
10 24 7 F Phenylalanine
14 49 3 P Proline
6 46 7 V Valine
18 63 11 R Arginine
9 31 1 Q Glutamine
9 55 11 E Glutamic acid
11 45 12 S Serine 

5LDP_1|Chains A, B|RNA 2',3'-cyclic phosphodiesterase|Escherichia coli BL21(DE3) (469008)
>7LYS_1|Chain A|CasPhi-2|Biggievirus Mos11 (1925777)
>1RHR_1|Chain A|Caspase-3|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 \(w=f(c)\)
5LDP , Knot 85 177 0.82 40 132 168 
GMSEPQRLFFAIDLPAEIREQIIHWRAKHFPPEAGRPVAADNLHLTLAFLGEVSAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQLANMLRSQAARSGCFQSNRPFHPHITLLRDASEAVTIPPPGFNWSYAVTEFTLYASSFARGRTRYTPLKRWALTQ
7LYS , Knot 288 763 0.83 40 286 690 
MPKPAVESEFSKVLKKHFPGERFRSSYMKRGGKILAAQGEEAVVAYLQGKSEEEPPNFQPPAKCHVVTKSRDFAEWPIMKASEAIQRYIYALSTTERAACKPGKSSESHAAWFAATGVSNHGYSHVQGLNLIFDHTLGRYDGVLKKVQLRNEKARARLESINASRADEGLPEIKAEEEEVATNETGHLLQPPGINPSFYVYQTISPQAYRPRDEIVLPPEYAGYVRDPNAPIPLGVVRNRCDIQKGCPGYIPEWQREAGTAISPKTGKAVTVPGLSPKKNKRMRRYWRSEKEKAQDALLVTVRIGTDWVVIDVRGLLRNARWRTIAPKDISLNALLDLFTGDPVIDVRRNIVTFTYTLDACGTYARKWTLKGKQTKATLDKLTATQTVALVAIDLGQTNPISAGISRVTQENGALQCEPLDRFTLPDDLLKDISAYRIAWDRNEEELRARSVEALPEAQQAEVRALDGVSKETARTQLCADFGLDPKRLPWDKMSSNTTFISEALLSNSVSRDQVFFTPAPKKGAKKKAPVEVMRKDRTWARAYKPRLSVEAQKLKNEALWALKRTSPEYLKLSRRKEELCRRSINYVIEKTRRRTQCQIVIPVIEDLNVRFFHGSGKRLPGWDNFFTAKKENRWFIQGLHKAFSDLRTHRSFYVFEVRPERTSITCPKCGHCEVGNRDGEAFQCLSCGKTCNADLDVATHNLTQVALTGKTMPKREEPRDAQGTAPARKTKKASKSKAPPAEREDQTPAQEPSQTSHHHHHH
1RHR , Knot 72 147 0.81 38 113 144 
SGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETD

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 \(c\).

\(|P_{f(5LDP_1)}(2) \setminus P_{f(7LYS_1)}(2)|=25\), \(|P_{f(7LYS_1)}(2) \setminus P_{f(5LDP_1)}(2)|=179\). 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 1:110010011111011101000110101001110110111100101011111010100001101111010011101010011011000111111001101110110110001100101000011010101100100110111111010011001010100110100000110011100
Pair \(Z_2\) Length of longest common subsequence
5LDP_1,7LYS_1 204 5
5LDP_1,1RHR_1 161 3
7LYS_1,1RHR_1 217 4

Newick tree

 
[
	7LYS_1:11.35,
	[
		5LDP_1:80.5,1RHR_1:80.5
	]:31.85
]

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 \((0.85)(0.8)(\frac{940 }{\log_{20} 940}-\frac{177}{\log_{20}177})=210.\)
Status Protein1 Protein2 d d1/2
Query variables 5LDP_1 7LYS_1 262 159.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]