CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4ZRI_1 3EWV_1 5XSY_1 Letter Amino acid
13 2 61 Y Tyrosine
20 11 104 A Alanine
18 8 148 I Isoleucine
34 9 187 L Leucine
30 8 95 K Lycine
18 8 127 F Phenylalanine
13 2 74 P Proline
6 0 31 W Tryptophan
18 7 135 V Valine
11 6 91 N Asparagine
19 17 94 D Aspartic acid
14 11 88 G Glycine
13 6 54 Q Glutamine
28 21 126 E Glutamic acid
7 7 17 H Histidine
15 4 112 S Serine
14 12 92 T Threonine
18 6 77 R Arginine
4 0 36 C Cysteine
11 9 71 M Methionine 

4ZRI_1|Chains A, B|Merlin|Homo sapiens (9606)
>3EWV_1|Chain A|Calmodulin|Homo sapiens (9606)
>5XSY_1|Chain A|Sodium channel protein|Electrophorus electricus (8005)
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 \(w=f(c)\)
4ZRI , Knot 145 324 0.86 40 210 310 
GPGSMAGAIASRMSFSSLKRKQPKTFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKIYCPPEASVLLASYAVQAKYGDYDPSVHKRGFLAQEELLPKRVINLYQMTPEMWEERITAWYAEHRGRARDEAEMEYLKIAQDLEMYGVNYFAIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIGNHDLFMRRRKADSLEVQQ
3EWV , Knot 69 154 0.75 36 99 136 
HHHHHHADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
5XSY , Knot 623 1820 0.85 40 362 1490 
MARKFSSARPEMFRRFTPDSLEEIEAFTELKKSCTLEKKEPESTPRIDLEAGKPLPMIYGDPPEDLLNIPLEDLDPFYKTQKTFIVISKGNIINRFNAERALYIFSPFNPIRRGAIRVFVNSAFNFFIMFTIFSNCIFMTISNPPAWSKIVEYTFTGIYTFEVIVKVLSRGFCIGHFTFLRDPWNWLDFSVVTMTYITEFIDLRNVSALRTFRVLRALKTITIFPGLKTIVRALIESMKQMGDVVILTVFSLAVFTLAGMQLFMGNLRHKCIRWPISNVTLDYESAYNTTFDFTAYIENEENQYFLDGALDALLCGNNSDAGKCPEGYTCMKAGRNPNYGYTNYDNFAWTFLCLFRLMLQDYWENLYQMTLRAAGKSYMVFFIMVIFLGSFYLINLILAVVAMAYEEQNQATLAEAQEKEAEFQRAVEQLRIQQEQINDERKASLASQLTQNQEAEITDDGDDAIKECNGKAFPLANIREPSSVKLSTEEQRSDSKSMDSKHSVDKPSLKHKAASTMSVFTLEDLEAARRPCPPVWYKFAGFVFKWNCCGPWVFLKKWVHFVMMDPFTDLFITLCIILNTLFMSIEHHPMNESFQSLLSAGNLVFTTIFAAEMVLKIIALDPYYYFQQTWNIFDSIIVSLSLLELGLSNMQGMSVLRSLRLLRIFKLAKSWPTLNILIKIICNSVGALGNLTIVLAIIVFIFALVGFQLFGKNYKEYVCKISDDCELPRWHMNDFFHSFLIVFRALCGEWIETMWDCMEVGGVPMCLAVYMMVIIIGNLVMLNLFLALLLSSFSSDNLSSIEEDDEVNSLQVASERISRAKNWVKIFITGTVQALVLWIQGKKPPSDDVVGEEGDNEGKKDTLPLNYLDGEKIVDGITNCVESPTLNLPIVKGESEIEEEGLVDSSDEEDTNKKKHALNDEDSSVCSTVDYSPSEQDPLAKEEEEEEEEEPEELESKDPEACFTEKCIWRFPFLDVDITQGKGKIWWNLRRTCYTIVEHDYFETFIIFMILLSSGVLAFEDIYIWRRRVIKVILEYADKVFTYVFIVEMLLKWVAYGFKRYFTDAWCWLDFVIVGASIMGITSSLLGYEELGAIKNLRTIRALRPLRALSRFEGMKVVVRALLGAIPSIMNVLLVCLMFWLIFSIMGVNLFAGKFYRCINTTTDEILPVEEVNNRSDCMALMYTNEVRWVNLKVNYDNAGMGYLSLLQVSTFKGWMDIMYAAVDSREVEDQPIYEINVYMYLYFVIFIVFGAFFTLNLFIGVIIDNFNRQKQKLGGEDLFMTEEQKKYYNAMKKLGSKKAAKCIPRPSNVVQGVVYDIVTQPFTDIFIMALICINMVAMMVESEDQSQVKKDILSQINVIFVIIFTVECLLKLLALRQYFFTVGWNVFDFAVVVISIIGLLLSDIIEKYFVSPTLFRVIRLARIARVLRLIRAAKGIRTLLFALMMSLPALFNIGLLLFLIMFIFSIFGMSNFAYVKKQGGVDDIFNFETFGNSMICLFEITTSAGWDGLLLPTLNTGPPDCDPDVENPGTDVRGNCGNPGKGITFFCSYIILSFLVVVNMYIAIILENFGVAQEESSDLLCEDDFVMFDETWHKFDVHGTQFLDYNDLPRFVNALQEPMRIPNPNRHKLAKMDMYVVMEDKISYLDVLLAVTQEVLGDTTEMEAMRLSIQAKFKKDNPSPTFFEPVVTTLRRKEEEWASVVIQRAFRQYLLMRAVSHASFLSQIKHMNEGPKDGVGSQDSLITQKMNALYRGNPELTMPLEQQIKPMLDKPRMPSLSVPETYPIQIPKEVTNEVILHSAPMVRQNYSYSGAIVVRESIV

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 \(c\).

\(|P_{f(4ZRI_1)}(2) \setminus P_{f(3EWV_1)}(2)|=144\), \(|P_{f(3EWV_1)}(2) \setminus P_{f(4ZRI_1)}(2)|=33\). 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 1:111011111100101001000010010101101010101000101010011011000111000111110001000111101000110001000011010111010100100011001000111101000110001001101011110011010010001010001111000111001101001010110001011010001010001010010110010101100111000010011111011110100100010101011100100100000010101100010110100001010011101011000111000010010100
Pair \(Z_2\) Length of longest common subsequence
4ZRI_1,3EWV_1 177 3
4ZRI_1,5XSY_1 172 6
3EWV_1,5XSY_1 269 4

Newick tree

 
[
	3EWV_1:12.72,
	[
		4ZRI_1:86,5XSY_1:86
	]:35.72
]

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 \((0.85)(0.8)(\frac{478 }{\log_{20} 478}-\frac{154}{\log_{20}154})=95.5\)
Status Protein1 Protein2 d d1/2
Query variables 4ZRI_1 3EWV_1 124 89
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]