Cellular Automata Model for Ribonucleic Acid (RNA)

Abstract

In the central dogma of biology, RNA bridges the gap between genomics and proteomics. CA rules are designed in Chap. 2 for RNA building blocks. This chapter reports how ‘equivalent CA rule groups’ model the ‘codon degeneracy’. Design of RCAM (RNA Modelling CA Machine) is covered in this chapter. RCAM evolution generates signal graphs. Algorithms are designed out of signal graph analytics. RCAM evolution of codon string of an mRNA molecule models the biological process of translation. Algorithms are constructed to predict co-translational folds and mutational effects. The predicted results are similar to the results reported out of wet lab experiments. From CA signal graph analytics, secondary structures are predicted for different class of RNA molecules—tRNA, RNA precursor, miRNA, etc. Predicted results are validated against the experimental results reported in web sites or research papers. Finally, the model for binding of siRNA molecule on its target gene is reported along with prediction of true positive and true negative instance reported in databases.

“I’m fascinated by the idea that genetics is digital. A gene is a long sequence of coded letters, like computer information. Modern biology is becoming very much a branch of information technology”.

—Richard Dawkins

Annexure

3.1.1 Annexure 3.1: Analysis of Nucleotide Bases to Assign Cellular Automata (CA) Rules

Section 3.3.3 reports the assignment of Cellular Automata (CA) rules to the codon triplets. Such an assignment demands detailed analysis of the atoms of different nucleotide bases and the associated sequence in different codons, as presented in this annexure.

The relevant features of the four nucleotide bases are retrieved from PubChem database (https://pubchem.ncbi.nlm.nih.gov/) which are analyzed in this annexure. The volume surface of Nitrogen (N), Oxygen (O), and Carbon (C) atom are reported as 15.3, 18.1 and 9.9, respectively as noted in the paper [24]. The polar positive, polar negative and non-polar surface areas for four bases are computed for each of the bases. The value of XLogP3 for G, A, U and C are −1.0, −0.1, −1.1 and −1.7, respectively. This value specifies how hydrophilic or hydrophobic a molecule is. Higher hydrophobicity is indicated by lesser negative value in the comparative scale for four bases.

Based on the analysis of these parameters, the bases are arranged in the following descending order: G > A > U > C with G and C, assigned maximum and minimum weight respectively. Among the bases, the atomic structure of base A stands apart from others since it does not have any oxygen atom in its atomic structure and so it does not have any negatively charged surface area. As per XLogP3 values, base A can be viewed as most hydrophobic, while C is least hydrophobic among the four bases.

For comparative analysis of 16 base pairs with left and middle base (first two bases), it has been assumed that the parameters of the left base play more dominant role. For example, the base A is assigned higher weight than the base C for the pair AC; on the other hand higher weight is assigned to C than A for the pair CA. Considering the special characteristics of base A, and the XLogP3 values, the 16 base pairs are divided into the following two groups.

• (i) The first group consists of the pairs GG, GU, GC, UC, CG, CU, CC, none of which covers the base A. In a comparative scale, these pairs are assumed to be neither hydrophilic nor hydrophobic. The base pair A followed by C is added in this list since A is least hydrophilic, while C is most hydrophilic.

• (ii) The second group covers the six base pairs involving base A that is least hydrophilic—GA, AA, UA, CA, AG and AU. These pairs are assumed to be either hydrophilic or hydrophilic. Two other base pairs UG and UU are added to this list since both U and G have similar XLogP3 values −1.1 and −1.0. Further, the base U displays polar positive surface area (30.6) and polar negative surface area (36.2).

The first group of base pairs are assigned to (2, 2) 4RGs having balanced rules subdivided as per the parameter value δ. The descending order of base pairs is derived based on higher weight to the left base and sum of polar surface area for each pair. Each pair is associated with an amino acid as per the parameter value δ elaborated next.

• δ = 1 GG > GU > GC > AC

• δ = 2 UC > CG > CU

• δ = 0 CC

The second group of base pairs are assigned to non-(2, 2) 4RGs (ID 9–16) with its subgroups detailed next. Each pair is associated with two or three amino acids including stop codons.

• δ = 1 GA > AA > UA > CA

• δ = 0 AG

• δ = 2 AU > UG

• δ = 0 UU

The base pairs are next assigned to different 4RGs, as reported in main text Sect. 3.3.3, based on the sum of decimal values of CA rules associated with 4RGs and parameter δ.

3.1.2 Annexure 3.2: Outline of CA Model for Post co-Translational Folding and Prediction of Protein Structure

CA model for co-translational folding is explained in Sect. 3.6. The algorithm designed to predict the fold points (of nascent peptide chain translated out of codon string) is reported along with the results derived on executing the software code developed for the algorithm.

We have experimented with the mRNA codon string of 16000 proteins retrieved from Dunbrack data set (http://dunbrack.fccc.edu) and designed two databases named as EFRL (Excluded Fold Residue Location) and VFRL (Valid Fold Residue Location). We predict true/false cases of prediction of fold residue location (FRL) for an input codon string based on these EFRL and VFRL databases. Based on the foundation laid down in Sect. 3.6 with the CA model for co-translational folding, we take the next step to model post-co-translational folding.

This annexure highlights the methodology we are implementing for post-co-translational folding and prediction of protein structure. We have assumed that during post-co-translational folding, secondary structures of helix and beta get introduced on protein chain. Each of helix and beta introduces folds at the start and end on the protein chain. In addition to the folds detected during co-translational folding, we add these new folds due to helix and beta. Fold Segments (FSs) are next derived with the amino acid residues between each pair of folds identified during co-translational and post-co-translational folding. On either end of such a segment dihedral angles of first and last two residues are noted. The Fold Segment Database (FSDB) designed out of large number of proteins lays the foundation for prediction of protein structure. The sequential steps of this methodology are noted below which are being finalized prior to development of the program.

Step 1: Develop the fold segment databases (FSDB0, FSDB1, FSDB2 and FSDB3) with the results of true VFRL, and FRL specified on first and last base of secondary structures of helix and beta noted in PDB for 16000 Dunbrack proteins.

• While FSDB0 covers, each of the segments derived out of 16000 proteins, the next three databases merge adjacent fold segments as follows.

• FSDB1 and FSDB2 merges each FSDB0 entry with the left and right neighbouring segments, respectively.

• The FSDB3 merges each of FSDB0 with its left and right neighbours. These databases have been designed.

• Each entry in FSDB records two dihedral angles of the first and last residue locations as explained in Sect. 3.6 while introducing two databases for EFRL (excluded FRL) and VFRL (valid FRL).

Step 2: Select three public domain packages for prediction of helix and beta in a protein chain.

Step 3: In order to predict three-dimensional structure of a candidate protein chain, we execute the Steps 4–7.

Step 4: Derive co-translational fold list out of VFRL (valid fold residue location) noted in Sect. 3.6.

Step 5: Run the three packages (noted in Step 2) to predict helix and beta structure in the candidate input chain. Identify helix and beta locations in the candidate chain based on majority voting of the results derived out of three packages. Based on location of helix and beta in the candidate chain, next step modifies the VFRL list.

Step 6: Modification of VFRL (Valid Fold Residue Location) list and derivation of composite VFRL for the candidate chain—mark a VFRL entry as ‘False’ if it is covered within a helix and beta excepting first and last two bases. Remove such ‘False’ entries. Subsequent to exclusion of such ‘False’ FRLs from VFRL, add additional folds at the start and end of location of each helix and beta. This is marked as composite VFRL List.

Step 7: Derive fold segments between each pair of folds noted in the composite VFRL list generated in Step 6.

Step 8: For each fold segment identified in Step 7, search FSDB (fold segment data base) designed in Step 1.

Step 9: Stitch the fold segments identified in Step 8 to predict the three-dimensional structure of the input candidate protein chain while taking into consideration the dihedral angle pairs noted for start and end residues of a segment. Stitching of a pair of adjacent segments extracted from FSDB demand search of correct options out of available multiple options.

3.1.3 Annexure 3.3: CS/CL Signal Graph of an Example RNA Molecule and Derivation of CrP (Critical Pair)

CS signal graph is derived out of Cycle Start (CS)/Cycle Length (CL) parameter table for an example RNA molecule having 159 nucleotide bases reported below. The column 1 and column 2 of the table below report the serial number of the nucleotide bases of the RNA. The CS and CL parameters derived out of ComRCAM are noted on column 3, 4 and on column 9, 10 on two major columns 1 to 6 and 7 to 12 respectively. The CS signal graph is derived by subtracting CS value of (i − 1)th cell from that of ith cell modelling respectively the (i − 1)th and ith location bases. The CS Difference (CSD) values are noted on column 5 and 11. Most of the CS difference values lie in the range 0 to −4, hence the threshold limit is set as −4. The CS difference value that is outside this range is marked as CrP (critical pair) reported on Col 6 and 12. For example, the first CrP in the list at location 28 is -32 since CS values for base location 27 is 372, while the value for location 28 is 340. A positive CS difference value outside the range of 0 to −4 is also marked as CrP as noted for location 62. The CrP values are analysed and processed in different algorithms reported in the main body of this chapter. Location of CrPs derived out of CS signal graphs provides the foundation of signal graphs analytics projected for different classes of RNA molecules.

The CS signal graph derived out of CS difference values is reported below for the RNA molecule. Signal graph analytics of such graphs represents various physical domain features of the RNA molecule as reported in different section of this chapter (Fig. 3.37).

Fig. 3.37

Cycle Start (CS) signal graph of RNA molecule with COMRCAM evolution

Pos	AA	CS Val	CL Val	CSD	CrP	Pos	AA	CS Val	CL Val	CSD	CrP
1	G	388	136			81	T	271	68	0
2	G	387	136	−1		82	T	271	68	0
3	C	387	136	0		83	T	270	68	−1
4	T	386	136	−1		84	A	270	68	0
5	C	386	136	0		85	A	269	68	−1
6	T	385	136	−1		86	T	269	68	0
7	A	385	136	0		87	T	268	68	−1
8	T	384	136	−1		88	A	267	68	−1
9	G	380	136	−4		89	G	267	68	0
10	G	380	136	0		90	C	267	68	0
11	C	380	136	0		91	T	266	68	−1
12	T	380	136	0		92	G	266	68	0
13	T	380	136	0		93	G	265	68	−1
14	A	380	136	0		94	G	265	68	0
15	G	380	136	0		95	A	264	68	−1
16	T	380	136	0		96	A	264	68	0
17	T	380	136	0		97	T	263	68	−1
18	G	379	136	−1		98	G	263	68	0
19	G	379	136	0		99	G	262	68	−1
20	T	378	136	−1		100	T	262	68	0
21	T	378	136	0		101	G	261	68	−1
22	A	377	136	−1		102	G	261	68	0
23	A	377	136	0		103	C	260	68	−1
24	A	376	136	−1		104	A	256	68	−4
25	G	372	136	−4		105	C	256	68	0
26	C	372	136	0		106	A	256	68	0
27	G	372	136	0		107	C	228	68	−28	CrP
28	C	340	136	−32	CrP	108	T	228	68	0
29	C	340	136	0		109	C	226	68	−2
30	T	339	136	−1		110	C	226	68	0
31	G	339	136	0		111	T	226	68	0
32	T	338	136	−1		112	G	226	68	0
33	C	338	136	0		113	T	226	68	0
34	T	337	136	−1		114	A	226	68	0
35	C	337	136	0		115	G	226	68	0
36	G	336	136	−1		116	T	211	68	−15	CrP
37	T	336	136	0		117	C	211	68	0
38	A	335	136	−1		118	C	210	68	−1
39	A	335	136	0		119	C	210	68	0
40	A	334	136	−1		120	A	209	68	−1
41	A	330	136	−4		121	G	209	68	0
42	A	330	136	0		122	C	208	68	−1
43	A	330	136	0		123	T	208	68	0
44	T	302	136	−28	CrP	124	A	207	68	−1
45	G	302	136	0		125	C	207	68	0
46	T	302	136	0		126	T	206	68	−1
47	C	302	136	0		127	C	206	68	0
48	A	302	136	0		128	A	205	68	−1
49	G	301	136	−1		129	G	205	68	0
50	C	299	136	−2		130	G	204	68	−1
51	C	295	136	−4		131	A	204	68	0
52	T	294	136	−1		132	G	203	68	−1
53	G	294	136	0		133	A	203	68	0
54	A	293	136	−1		134	C	202	68	−1
55	G	293	136	0		135	T	202	68	0
56	C	292	136	−1		136	G	201	68	−1
57	A	288	136	−4		137	A	201	68	0
58	A	288	136	0		138	A	200	68	−1
59	C	288	136	0		139	G	200	68	0
60	A	282	136	−6	CrP	140	C	199	68	−1
61	T	281	136	−1		141	A	199	68	0
62	T	282	136	1	CrP	142	G	198	68	−1
63	T	282	136	0		143	G	194	68	−4
64	C	282	136	0		144	A	194	68	0
65	T	282	136	0		145	G	194	68	0
66	A	282	136	0		146	G	194	68	0
67	C	282	136	0		147	A	194	68	0
68	A	282	136	0		148	T	194	68	0
69	A	280	136	−2		149	C	194	68	0
70	A	280	136	0		150	G	194	68	0
71	T	280	136	0		151	C	194	68	0
72	T	279	136	−1		152	T	193	68	−1
73	A	279	136	0		153	T	193	68	0
74	T	275	136	−4		154	G	192	68	−1
75	T	274	68	−1		155	A	192	68	0
76	A	274	68	0		156	G	191	68	−1
77	T	273	68	−1		157	C	191	68	0
78	T	273	68	0		158	C	190	68	−1
79	T	272	68	−1		159	C	181	68	−9	CrP
80	T	271	68	−1

3.1.4 Annexure 3.4: Predicted tRNA Secondary Structures for tRNA Sequences Retrieved from the Database - GtRNAdb.ucsc.edu

The algorithim to predict secondary structure of a tRNA molecule is reported in Sect. 3.7.1. Representative results are reported in Figs. 3.12 and 3.13. The algorithm has been coded and executed for large number base sequences of tRNA molecules of different species. The predicted results are tabulated below. The basic structure of tRNA molecule for wide variety of species is identical with three loops D, T, anticodon loops and variable length V loop.

Name	Accepter	D Stem	D Loop	D Stem	A Stem	A Loop	A Stem	V Loop	T Stem	T Loop	T Stem	Stem
chr19trna13	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–48	49–51	52–62	63–65	66–72
chr1trna50	1–5	10–12	13–22	23–25	27–31	32–38	39–43	44–47	48–52	53–60	61–65	68–72
chr6trna125	2–7	10–12	13–22	23–25	27–31	32–38	39–43	44–49	50–52	53–61	62–64	66–71
chr6trna126	1–3	5–7	8–12	13–15	28–32	33–39	40–44	45–49	50–52	53–63	64–66	71–73
chr6trna127	1–3	6–8	9–24	25–27	28–32	33–39	40–44	45–59	60–62	63–69	70–72	73–75
chr6trna122	1–3	10–12	13–23	24–26	28–32	33–39	40–44	45–49	50–52	53–63	64–66	71–73
chr2trna13	1–7	15–17	18–22	23–25	27–31	32–42	43–47	48–68	69–73	74–80	81–85	86–92
chr2trna12	1–7	10–12	13–17	18–20	22–26	27–33	34–38	39–42	43–47	48–53	54–58	59–65
chr2trna17	1–7	11–13	14–20	21–23	28–34	35–33	34–40	41–46	47–49	50–60	61–63	64–70
chr19trna14	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–47	48–50	51–62	63–65	66–72
chr6trna9	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–48	49–51	52–62	63–65	66–72
chr1trna78	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–48	49–51	52–62	63–65	66–72
chr8trna5	4–7	9–11	12–18	19–21	23–27	28–35	36–40	41–44	45–49	50–56	57–61	62–65
chr8trna2	1–7	10–12	13–22	23–25	27–31	32–42	43–47	48–66	67–69	70–75	76–78	86–92
chr8trna1	1–3	11–13	14–18	19–21	28–30	31–34	35–37	38–46	47–49	50–64	65–67	68–70
chr8trna9	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–57	58–60	61–71	72–74	75–81
chr8trna8	1–3	10–12	13–22	23–25	27–30	31–39	40–43	44–48	49–52	53–61	62–65	70–72
chr6trna95	1–4	10–12	13–22	23–25	27–31	32–38	39–43	44–48	49–51	52–58	59–61	62–65
chr6trna94	4–6	10–12	13–22	23–25	29–33	34–36	37–41	42–48	49–51	52–62	63–65	70–72
chr6trna97	1–3	5–7	8–16	17–19	27–30	31–39	40–43	44–47	48–50	51–65	66–68	70–72
chr6trna96	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–47	48–50	51–62	63–65	66–72
chr6trna91	1–7	11–13	14–18	19–21	27–30	31–39	40–43	44–48	49–51	52–62	63–65	66–72
chr6trna93	1–3	11–13	14–21	22–24	27–31	32–38	39–43	44–48	49–53	54–60	61–65	67–69
chr6trna99	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–47	48–50	51–61	62–64	65–71
chr6trna98	1–3	10–12	13–23	24–26	28–32	33–39	40–44	45–59	60–62	63–69	70–72	73–75
chr16trna8	1–4	6–8	9–22	23–25	27–31	32–38	39–43	44–47	48–52	53–61	62–66	69–72
chr16trna6	1–3	6–8	9–22	23–25	27–31	32–38	39–43	44–47	48–52	53–61	62–66	70–72
chr16trna1	1–3	7–9	10–16	17–19	27–31	32–38	39–43	44–48	49–52	53–61	62–65	69–71
chr16trna3	2–7	10–12	13–22	23–25	28–31	32–38	39–42	43–48	49–53	54–60	61–65	66–71
chr1trna98	1–3	10–12	13–23	24–26	28–32	33–39	40–44	45–52	53–55	56–63	64–66	71–73
chr1trna99	1–5	12–14	15–19	20–22	28–31	32–35	36–39	40–48	49–52	53–59	60–63	67–71
chr12trna15	1–5	7–9	10–24	25–27	29–34	35–39	40–45	46–57	58–60	61–66	67–69	70–74
chr1trna92	1–3	12–14	15–19	20–22	28–31	32–38	39–42	43–44	45–47	48–61	62–64	70–72
chr12trna10	1–3	12–14	15–22	23–25	27–31	32–38	39–43	44–53	54–56	57–62	63–65	69–71
chr12trna12	1–3	12–14	15–22	23–25	27–31	32–38	39–43	44–53	54–56	57–62	63–65	69–71
chr2trna18	1–7	12–14	15–19	20–22	30–32	33–36	37–39	40–47	48–51	52–60	61–64	65–71
chrXtrna10	1–7	10–12	13–23	24–26	28–32	33–39	40–44	45–49	50–52	53–63	64–66	67–73
chr6trna128	1–7	10–12	13–23	24–26	28–32	33–39	40–44	45–49	50–52	53–63	64–66	67–73
chr7trna29	1–5	10–12	13–21	22–24	27–30	31–37	38–41	42–47	48–51	52–60	61–64	67–71
chr15trna8	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–47	48–50	51–61	62–64	65–71
chr15trna9	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–47	48–51	52–60	61–64	65–71
chr6trna50	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–57	58–60	61–71	72–74	75–81
chr7trna21	1–5	10–12	13–21	22–24	27–30	31–37	38–41	42–47	48–51	52–60	61–64	67–71
chr7trna20	1–4	10–12	13–21	22–24	26–30	31–37	38–42	43–47	48–50	51–61	62–64	67–70
chr7trna23	1–5	10–12	13–21	22–24	26–30	31–37	38–42	43–47	48–51	52–60	61–64	67–71
chr7trna22	1–3	10–12	13–21	22–24	27–30	31–37	38–41	42–48	49–51	52–60	61–63	69–71
chr15trna1	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–47	48–51	52–60	61–64	65–71
chr15trna3	1–5	10–12	13–22	23–25	28–31	32–38	39–42	43–48	49–52	53–61	62–65	68–72
chr19trna3	1–3	11–13	14–22	23–25	30–36	37–35	36–42	43–47	48–53	54–62	63–68	71–73
chr19trna4	1–3	5–7	8–15	16–18	26–31	32–38	39–44	45–49	50–52	53–57	58–60	65–67
chr6trna54	1–7	9–11	12–25	26–28	29–33	34–36	37–41	42–49	50–54	55–61	62–66	67–73
chr19trna6	2–7	10–12	13–22	23–25	29–33	34–36	37–41	42–49	50–52	53–61	62–64	66–71
chr6trna56	2–4	6–8	9–14	15–17	29–31	32–38	39–41	42–33	34–36	37–61	62–64	65–67
chr6trna59	1–3	10–12	13–23	24–26	28–32	33–39	40–44	45–55	56–58	59–66	67–69	71–73
chr6trna168	1–3	10–12	13–23	24–26	28–32	33–39	40–44	45–49	50–52	53–63	64–66	71–73
chr5trna5	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–48	49–51	52–62	63–65	66–72
chr6trna159	1–4	10–12	13–23	24–26	31–30	31–40	41–40	41–50	51–53	54–62	63–65	70–73
chr6trna158	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–47	48–54	55–59	60–66	66–72
chr6trna155	1–4	10–12	13–23	24–26	31–30	31–40	41–40	41–50	51–53	54–62	63–65	70–73
chr6trna154	1–3	10–12	13–23	24–26	31–30	31–40	41–40	41–50	51–53	54–62	63–65	71–73
chr6trna157	3–7	10–12	13–22	23–25	27–31	32–38	39–43	44–48	49–53	54–60	61–65	66–70
chr6trna151	1–7	11–13	14–20	21–23	26–30	31–37	38–42	43–51	52–54	55–61	62–64	65–71
chr6trna150	1–6	10–12	13–22	23–25	27–31	32–38	39–43	44–48	49–51	52–62	63–65	67–72
chr6trna153	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–48	49–51	52–62	63–65	66–72
chr6trna51	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–57	58–60	61–71	72–74	75–81
chr19trna1	1–3	10–12	13–23	24–26	28–32	33–39	40–44	45–52	53–55	56–63	64–66	71–73
chr19trna2	1–7	11–13	14–23	24–26	28–31	32–38	39–42	43–47	48–52	53–59	60–64	65–71
chr1trna59	1–4	10–12	13–24	25–27	30–33	34–40	41–44	45–59	60–64	65–71	72–76	80–83
chr9trna1	1–7	9–11	12–24	25–27	30–33	34–40	41–44	45–54	55–58	59–63	64–67	68–74
chr9trna1	1–7	11–13	14–20	21–23	25–28	29–45	46–49	50–54	55–58	59–63	64–67	68–74
chr6trna137	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–47	48–50	51–61	62–64	66–72
chr1trna118	1–5	10–13	14–22	23–26	29–33	34–44	45–49	50–136	137–140	141–149	150–153	154–158
chrXtrna1	1–3	6–8	9–23	24–26	27–32	33–37	38–43	44–47	48–51	52–60	61–64	69–71
chr6trna28	1–7	10–12	13–23	24–26	41–43	44–50	51–53	54–69	70–72	73–83	84–86	87–93
chr6trna44	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–57	58–60	61–71	72–74	75–81
chr14trna19	1–7	10–12	13–22	23–25	33–35	36–46	47–49	50–69	70–72	73–83	84–86	87–93
chr17trna41	1–7	10–12	13–22	23–25	27–31	32–38	39–43	44–57	58–61	62–70	71–74	75–81

3.1.5 Annexure 3.5: Predicted Results for Binding of siRNA Molecules on RNA Transcript of Target Gene

The algorithm to predict binding of siRNA with target gene is reported in Sect. 3.8.

Table 3.24 reports sample prediction results for ten cases derived on execution of the program code for the algorithm. The siRNA/gene ID is noted on column 1. The next table reports a number of prediction results (DOM) on last column for siRNA and target gene retrieved from NCBI Probe database [22].

siRNA ID/Gene ID	M′	LOM	M	ROM	LOM′/ROM′	LOM/ROM	DOM
8811589b/UBE2T	19	300–317	318		0/0	0/0	0
8812102b/UBE2E3	8	518–524	525	526–536	0/0	0/1	1
8812967b/P2RX3	–	586–590	591	592–604	0/0	0/1	1
8811547b/UFC1	19	114–131	132		1/0	0/0	1
8811418b/UBE2L6	15	437–450	451	452–455	1/0	0/0	1
8811391b/UBE2S	19	160–177	178		0/0	1/0	0
8811310b/UBE2I	8	155–161	162	163–173	0/0	0/0	0
8812922b/P2RX3	5	326–329	330	331–344	0/0	0/1	1
8817061b/PHF19	19	1565–1582	1583		0/0	0/0	0
8810803b/UBE2 M	4	414–416	417	418–432	0/1	0/2	1
8810630b/UBE2D3	12	332–342	343	344–350	0/0	0/0	0
8811746b/UBE2J1	19	489–506	507		1/0	1/0	0
8812175b/UBE2V1	19	444–461	462		0/0	3/0	1
8811576b/UBE2T	15	472–485	486	487–490	1/0	0/0	1
8811073b/RAB6IP1	19	3672–3689	3690		0/0	1/0	1
8811496b/UFC1	4	–	–	–	0/0	0/0	0
8812990b/P2RX3	19	108–125	126		2/0	0/0	1
8811406b/UBE2S	10	88–96	97	98–106	1/1	1/0	1
8812149b/UBE2E3	–	227–227	228	229–245	0/0	0/2	1
8811687b/UBE2 W	–	258–262	263	264–276	0/0	0/0	0
8811792b/UBE2 K	19	330–347	348		1/0	0/0	1
8811775b/UBE2 K	19	382–399	400		0/0	0/0	0
8817034b/CYP4Z1	15	1314–1327	1328	1329–1332	1/0	0/1	2
8817011b/OR12D3	19	–	–	–	0/0	0/0	0
8811564b/UBE2T	19	537–554	555		0/0	2/0	1
8811442b/UBE2L6	–	262–266	267	268–280	0/0	0/0	0
8812959b/P2RX3	19	670–687	688		0/0	0/0	0
8810822b/UBE2 M	15	279–292	293	294–297	1/0	2/0	1
8811779b/UBE2 K	13	388–399	400	401–406	0/0	0/0	0
8812723b/SOST	–	212–226	227	228–230	0/0	0/0	0
8812136b/UBE2E3	8	366–372	373	374–384	0/0	0/1	1
8810843b/UBE2 M	11	118–127	128	129–136	0/1	0/1	0
8810821b/UBE2 M	–	291–292	293	294–309	0/0	0/0	0
8812738b/SOST	–	109–109	110	111–127	0/0	0/1	1
8811513b/UFC1	15	310–323	324	325–328	1/0	0/0	1
8811561b/UBE2T	19	537–554	555		0/0	2/0	1
8810642b/UBE2D3	9	284–291	292	293–302	0/0	1/0	1
8812124b/UBE2E3	19	383–400	401		0/0	0/0	0
8811205b/UBE2H	–	452–455	456	457–470	0/0	0/1	1
8811017b/RAB6IP1	7	3046–3051	3052	3053–3064	0/1	0/0	1
8810855b/UBE2 M	5	69–72	73	74–87	0/1	0/1	0
8812094b/UBE2E3	19	563–580	581		0/0	2/0	1
8812027b/UBE2G1	–	425–435	436	437–443	0/0	0/0	0
8811703b/UBE2 W	–	221–226	227	228–239	0/0	0/0	0
8817021b/KCNT1	19	1336–1353	1354		0/0	1/0	1
8811319b/UBE2I	19	116–133	134		0/0	0/0	0
8811622b/UBE2T	8	184–190	191	192–202	0/0	1/0	0
8817088b/DVL2	15	785–798	799	800–803	0/0	0/0	0
8810760b/UBE2B	–	187–188	189	190–205	0/0	0/1	1
8811283b/UBE2I	19	313–330	331		0/0	0/0	0

3.1.6 Annexure 3.6: Fold Residue Prediction

Section 3.6.2 showed a partial table in Table 3.9 with a partial number of residues. The next table shows the complete results for prediction of Fold Residue Location (FRL) for mRNA codon string of length 217, transcripted out of Gene ID CAA33815, Uniprot ID for the protein synthesized is P13342, PDB ID 1C1K.

(1) Pos	(2) IFRL prediction	(3) VFRL fold points	(4) SS motifs as noted in PDB	(5) Comment	(1) Pos	(2) IFRL prediction	(3) VFRL fold points	(4) SS motifs as noted in PDB	(5) Comment
1			–		110			H
2			E		111			H
3	1*	1	E	True	112			H
4			E		113			H
5			–		114			H
6			–		115			H
7			–		116			H
8			S		117			H
9			–		118			H
10	1*	1	T	True	119			H
11			T		120			H
12			–		121			H
13			–		122			H
14			–		123			H
15	1*	1	–	True	124			H
16			H		125			H
17			H		126			H
18			H		127			T
19			H		128			T
20			H		129			–
21			H		130			S
22			H		131			S
23			H		132			G
24			H		133			G
25			H		134			G
26			H		135			G
27			H		136			T
28			H		137			S
29			H		138			–
30	1*	1	H	True	139			B
31			T		140			T
32			T		141			T
33	1*	1	S	True	142			T
34			–		143			T
35			–		144			B
36			T		145			–
37			T		146			H
38			T		147			H
39			T		148			H
40			T		149			H
41			T		150			H
42			–		151	1*	1	H	True
43			–		152			H
44			–		153			T
45	1*	1	–	True	154	1*	1	T	True
46			–		155			S
47			H		156	1*	1	S	True
48			H		157			–
49			H		158			H
50			H		159			H
51			H		160			H
52			H		161			H
53			–		162			H
54			S		163			H
55			–		164			H
56			H		165			H
57			H		166			H
58			H		167			H
59			H		168			H
60			H		169	1*	1	–	True
61			H		170			H
62			H		171			H
63			H		172			H
64			H		173			H
65			H		174			H
66			–		175			H
67			–		176			H
68			H		177			H
69			H		178			–
70			H		179			–
71			H		180			–
72			H		181			H
73			H		182	1*	1	H	True
74			H		183			H
75	1*		H	False	184	1*		H	False
76			H		185			H
77			H		186			H
78			H		187			H
79			H		188			H
80			H		189			H
81			H		190			H
82			–		191			H
83			H		192			H
84			H		193			H
85			H		194			H
86			H		195			H
87	1*	1	S	True	196			H
88			S		197			E
89			–		198			E
90			G		199			E
91			G		200			–
92			G		201	1*	1	H	True
93			T		202			H
94			T		203			H
95			H		204	1*		H	False
96			H		205			H
97			H		206			H
98			H		207			H
99			H		208			H
100			H		209			H
101			H		210			H
102			H		211			H
103			H		212			H
104			H		213			H
105			H		214	1*	1	H	False
106			H		215			H
107	1*	1	H	True	216			H
108			T		217			–
109			H