AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions

Abstract

Background

Replication origins are considered important sites for understanding the molecular mechanisms involved in DNA replication. Many computational methods have been developed for predicting their locations in archaeal, bacterial and eukaryotic genomes. However, a prediction method designed for a particular kind of genomes might not work well for another. In this paper, we propose the AT excursion method, which is a score-based approach, to quantify local AT abundance in genomic sequences and use the identified high scoring segments for predicting replication origins. This method has the advantages of requiring no preset window size and having rigorous criteria to evaluate statistical significance of high scoring segments.

Results

We have evaluated the AT excursion method by checking its predictions against known replication origins in herpesviruses and comparing its performance with an existing base weighted score method (BWS₁). Out of 43 known origins, 39 are predicted by either one or the other method and 26 origins are predicted by both. The excursion method identifies six origins not predicted by BWS₁, showing that the AT excursion method is a valuable complement to BWS₁. We have also applied the AT excursion method to two other families of double stranded DNA viruses, the poxviruses and iridoviruses, of which very few replication origins are documented in the public domain. The prediction results are made available as supplementary materials at [1]. Preliminary investigation shows that the proposed method works well on some larger genomes too.

Conclusion

The AT excursion method will be a useful computational tool for identifying replication origins in a variety of genomic sequences.

Background

Recent advances in biotechnology have rendered sequencing a complete genome routine. With the increasing availability of DNA sequences, computational methods to predict likely locations of important functional sites before experimental search are highly valuable because the computational predictions can often help design finely tuned experiments to find these functional sites in shorter time with less labor and fewer resources. Replication origins, which are places on the DNA molecules where replication processes are initiated, are considered important sites for understanding the molecular mechanisms involved in DNA replication. For some viruses with double stranded DNA (dsDNA) genomes in particular, detailed knowledge of their replication processes have had significant impact in developing effective strategies to control the growth and spread of viruses (see, for example, [2]).

A number of computational methods have been developed for predicting replication origins in bacterial, archaeal, and eukaryotic genomes. All these algorithms exploit certain characteristic sequence features found around the replication origins. For example, Lobry [3] employs the GC skew plot to predict replication origins and terminus in bacterial genomes. The skew (G-C)/(G+C), where G and C respectively stand for the percentages of guanine and cytosine bases in a sliding window, switches polarity in the vicinity of the replication origin and terminus, with the leading strand manifesting a positive skew. Salzberg et al. [4] predict the replication origins for a number of bacterial and archaeal genomes by identifying some 7-mers and/or 8-mers whose orientation is preferentially skewed around the replication origins. Zhang and Zhang [5] use the Z-curve method successfully to identify several replication origins in bacterial and archaeal genomes. The Z-curve of any given DNA sequence is a three-dimensional curve which uniquely represents the sequence so that unusual sequence compositional features, such as those around a replication origin, can sometimes be visually recognized. Mackiewicz et al. [6] propose three methods, based on DNA asymmetry, the distribution of DnaA boxes and dnaA gene location, were applied to identify the putative replication origins in 112 bacterial chromosomes. They find that DNA asymmetry is the most universal method of putative oriC identification and better prediction can be achieved when the method is applied together with others.

For eukaryotic DNA, Breier et al. [7] develop the Oriscan algorithm to predict replication origins in the S. cerevisiae genome by searching for sequences similar to a training set of 26 known yeast origins pinpointed by site-directed mutagenesis. Oriscan uses both the origin recognition complex binding site and its flanking regions to identify candidates, and then ranks potential origins by their likelihood of activity. More recently, wavelet based multi-scale analysis of DNA strand asymmetries have also been developed [8,9] for detecting mammalian DNA replication origins.

It is important to note that a prediction method designed for one kind of genomes may not necessarily work well on others because the differences in DNA replication mechanisms in different organisms naturally lead to differences in sequence features around their replication origins. One would not expect that the prediction methods designed for bacterial, archaeal, and eukaryotic genomes can be applied directly to viral genomes and produce accurate results. Indeed, when we attempted to use the above algorithms on some herpesviruses genomes with known replication origins like those listed in Table 5 of [10], a variety of difficulties were encountered. For instance, no clear cut switches of polarity were observed in the GC skew plot. No definitive peaks can be visually identified from the Z-curves as potential replication origins of the viruses. When we mined for DnaA boxes [6] in the herpesviruses, just one cluster of DnaA boxes was observed, but it is not near to any known replication origins. Information about origin recognition complex binding sites for herpesvirus genomes, needed for applying Oriscan, are not readily available. While the method based on oligomers skew [4] is designed to work for genomes with single replication origins, the herpesviruses and many other dsDNA viruses contain multiple replication origins in their genomes.

Computational prediction of replication origins, based on the observation of a high concentration of palindromes around the origins, for dsDNA viral genomes was first attempted by Masse et al. [11] on the human cytomegalovirus. Leung et al. [10] formalize the procedure by laying down the mathematical foundation to justify the use of scan statistics for identifying statistically significant palindrome clusters. The location of such palindrome clusters are then taken to be the likely locations of replication origins in herpesviruses. Viewing the scan statistics approach as equivalent to counting the palindromes in sliding windows, Chew et al. [12] offer two more refined schemes of quantifying palindrome concentration to improve the sensitivity of the prediction. One of these schemes, namely the base weighted scheme (BWS₁), which scores each palindrome according to how rarely it is expected to occur in a nucleotide sequence generated randomly as a first order Markov chain, is found to be the most sensitive for the herpesviruses.

Because of the lack of strong family-wide sequence similarities around the origins, the above prediction methods designed for relatively large and complex dsDNA viruses like the herpesviruses with over 100,000 base pairs in the genomes are based on various sequence statistics rather than the actual nucleotide sequences around replication origins.

Herpesviruses utilize two different types of replication origins during lytic and latent infections. For each type of origins, the count and locations in the genome vary from one kind of herpesvirus to another. Most herpesviruses have one to two copies of latent and lytic origins. It has been documented in various studies (e.g. [11,13,14]) that the nucleotide sequences around the replication origins are specific to the individual viruses. Yet the presence of clusters of direct or inverted repetitive sequences, including palindromes, is quite common in both types of origins in many members of the herpesvirus family (see [12] and references therein).

Lin et al [15] have observed that in some herpesvirus genomes, the nucleotide sequences around replication origins are richer in A and T bases. This is not surprising because DNA replication typically requires the binding of an assembly of enzymes (e.g., helicases) to locally unwind the DNA helical structure, and pull apart the two complementary strands (see Chapter 1 in [16,17]). Higher AT content around the origins makes the two complementary DNA strands bond less strongly to each other. This facilitates the two strands to be pulled apart and initiate the replication process. Indeed, Segurado et al. [18] have used a sliding window approach to find "islands" within the Schizosaccharomyces pombe genome that have high AT content. They measure base composition using sliding windows of different sizes and find that AT content of windows in regions containing replication origins are significantly higher than those that do not.

Chew et al. [12] have also reported using sliding windows of AT percentages on herpesviruses. Using windows with top AT percentages they are able to predict 65% of replication origins in their dataset. Moreover, this method has successfully identified four origins not predicted by BWS₁, suggesting that the AT percentages may be a useful sequence feature to be incorporated into the set of replication origin prediction tools for dsDNA viruses. This motivates us to seek a means to better quantify the AT content variation in genome sequences. We find that the general score based excursion approach first proposed by Karlin and Altschul in [19] fits our purpose very well when it is applied appropriately to quantify local AT abundance. The excursion approach has the advantages of not requiring a preset sliding window size and having rigorous criteria to evaluate statistical significance of high scoring segments [20-22].

There are three main objectives in this paper. First, we shall develop the AT excursion method as a possible alternative to existing approaches for replication origin prediction in DNA sequences. Second, we shall assess the performance of AT excursion in comparison with the prediction results of BWS₁ on a data set of currently known origins of the herpesviruses. The herpes family is chosen as it is one of the bigger families of viruses with known replication origins so that the performance of our prediction method can be assessed. Our results demonstrate that the AT excursion method not only can compare with but can also complement the BWS₁ predictions very well. Having established that AT excursion method is a credible prediction tool, our third objective is to use it for predicting likely replication origin locations for two other families of dsDNA viruses, namely the poxviruses and iridoviruses of which very few replication origins are documented in the public domain. To demonstrate the generality of the AT excursion approach, we also apply it to several larger genomes.

Methods

We adopt the score-based excursion approach [19] to identify segments of a genome having high AT concentration. This, in turn, forms the basis of our proposed method to predict replication origins for the herpesviruses. Table 1 presents the viruses to be analyzed. The data set comprises all complete genome sequences of the herpesvirus family downloaded from GenBank at the NCBI web site in March 2006. For each virus, we list its abbreviation, accession number, sequence length, and AT percentages.

Table 1.

The list of herpesviruses to be analyzed.

Virus	Abbrev.	Accession	Length	AT%
Alcelaphine herpesvirus 1	alhv1	NC_002531	130608	53
Ateline herpesvirus 3	athv3	NC_001987	108409	63
Bovine herpesvirus 1	bohv1	NC_001847	135301	28
Bovine herpesvirus 4	bohv4	NC_002665	108873	59
Bovine herpesvirus 5	bohv5	NC_005261	138390	25
Callitrichine herpesvirus 3	calhv3	NC_004367	149696	51
Cercopithecine herpesvirus 1	cehv1	NC_004812	156789	26
Cercopithecine herpesvirus 2	cehv2	NC_006560	150715	24
Cercopithecine herpesvirus 8	cehv8	NC_006150	221454	51
Cercopithecine herpesvirus 9	cehv7	NC_002686	124138	59
Cercopithecine herpesvirus 15	cehv15	NC_006146	171096	38
Cercopithecine herpesvirus 16	cehv16	NC_007653	156487	24
Cercopithecine herpesvirus 17	mmrv	NC_003401	133719	47
Equid herpesvirus 1	ehv1	NC_001491	150224	44
Equid herpesvirus 2	ehv2	NC_001650	184427	43
Equid herpesvirus 4	ehv4	NC_001844	145597	50
Gallid herpesvirus 1	gahv1	NC_006623	148687	52
Gallid herpesvirus 2	gahv2	NC_002229	174077	56
Gallid herpesvirus 3	gahv3	NC_002577	164270	46
Human herpesvirus 1	hsv1	NC_001806	152261	32
Human herpesvirus 2	hsv2	NC_001798	154746	30
Human herpesvirus 3	vzv	NC_001348	124884	54
Human herpesvirus 4	ebv	NC_007605	171823	41
Human herpesvirus 5 (AD169)	hcmv	NC_001347	230287	43
Human herpesvirus 5 (Merlin)	hcmv-m	NC_006273	235645	42
Human herpesvirus 6	hhv6	NC_001664	159321	58
Human herpesvirus 6B	hhv6b	NC_000898	162114	58
Human herpesvirus 7	hhv7	NC_001716	153080	63
Human herpesvirus 8	hhv8	NC_003409	137508	47
Ictalurid herpesvirus 1	ichv1	NC_001493	134226	43
Meleagrid herpesvirus 1	mehv1	NC_002641	159160	52
Murid herpesvirus 1	mcmv	NC_004065	230278	41
Murid herpesvirus 2	rcmv	NC_002512	230138	39
Murid herpesvirus 4	muhv4	NC_001826	119450	53
Macaca fuscata rhadinovirus	mfrv	NC_007016	131217	48
Ostreid herpesvirus 1	oshv1	NC_005881	207439	61
Ovine herpesvirus 2	ohv2	NC_007646	135135	47
Pongine herpesvirus 4	ccmv	NC_003521	241087	38
Psittacid herpesvirus 1	pshv1	NC_005264	163025	39
Saimiriine herpesvirus 2	sahv2	NC_001350	112930	65
Suid herpesvirus 1	shv1	NC_006151	143461	26
Tupaiid herpesvirus 1	thv	NC_002794	195859	34

Score-based sequence analysis

Score-based sequence analysis is a powerful and yet flexible tool to identify segments of a biological (DNA, RNA or amino acids) sequence containing high concentration of residues of interest according to the users' objectives. One assigns high positive scores to residues of interest, high negative scores to contrasting residues and low or zero scores for the rest. Using various score schemes, Karlin and his collaborators applied this approach with success to gene finding, identification of transmembrane protein segments, and DNA-binding domains. For details and other applications, see, for example, [20-22] and the references therein.

Our interest in this paper is to identify segments of genomic sequences with high AT content. Towards this end, we label bases C or G as "strongly bonding" base S; and bases A or T as "weakly bonding" base W. Under this label, S bases (i.e., C or G) are given a score of s and W bases (i.e., A or T) a score of w. The scores s and w will be specified below. We next model the genomic sequence as a realization of a sequence of independent and identically distributed random variables, X₁, X₂, ..., X_n (where n is the genome length), taking values in {s, w}. If the ith base is labeled as W, X_i is given a score w otherwise X_i = s. We let p := P(X_i = s) and P (X_i = w) = 1 - p (denoted by q). The parameter p is naturally estimated by the CG percentage in the genome. An additional constraint needed to be imposed on the choice of s and w is that the expected score per base μ = ps + qw has to be negative. This condition prevents favoring long segments to be high scoring segments. A moment's reflection shows that we can always standardize one of the scores to be 1. Here we let w = 1 and choose s to be a negative integer (integer-value choice due to a technical reason as pointed out after equation (3)) so that the expected score per base, μ = ps + qw is close to the value of -0.5 (where we adopt Karlin's choice of expected value as in [21]). In other words, w := 1 and

$$s:=\lfloor \frac{\mu -qw}{p}\rfloor ,$$

where μ = -0.5 and ⌊·⌋ denotes the integer floor function.

Excursions and their values

We next compute the cumulative scores and seek to identify segments of the genome that have significantly high scores. As we are only interested in segments with positive additive scores, we reset our cumulative scores to zero whenever it becomes negative.

The excursion scores E_i's are defined recursively as

E₀ = 0, E_i = max{E_i-1 + X_i, 0}, for 1 ≤ i ≤ n.

Using this recursive definition, we are able to construct "excursions" for each of the genomes. An excursion starts at a point i where E_i is zero and ends at j > i where E_j is the very next zero. The score then stays at zero until it first becomes positive again for the start of the next excursion. The value of an excursion is defined to be the peak score during the course of that particular excursion.

Distribution of the Maximal Aggregate Score

For each value of x, the maximal aggregate score

$$M_n=\underset{1\le k\le n}{\max }{E}_k$$

satisfies

$$P\left(M_n>\frac{\ln n}{{\lambda }^{\ast }}+x\right)\approx 1-\exp \{-K^{\ast }{e}^{-{\lambda }^{*}x}\},$$

where λ* is the unique positive solution to the equation $E\left(e^{\lambda X_1}\right)$ = pe^λs + qe^λw = 1 and K* is a parameter given by an explicit series expansion (See [23]).

When X is an integer-valued variable of span δ, we have a simpler expression for K* ([23]):

$$\begin{array}{c}\exp \{-K_{+}{e}^{-\lambda \ast x}\}\le \underset{n\to \infty }{\lim \inf }P\left(M_n-\frac{\ln n}{\lambda *}<x\right)\\ \le \underset{n\to \infty }{\lim \sup }P\left(M_n-\frac{\ln n}{\lambda *}<x\right)\\ \le \exp \{-K_{-}{e}^{-\lambda *x}\},\end{array}$$

where

$$K_{-}=\frac{{\lambda }^{*}\delta }{e^{{\lambda }^{*}\delta }-1}{K}^{*},K_{+}=\frac{{\lambda }^{*}\delta }{1-e^{-{\lambda }^{*}\delta }}{K}^{*}.$$

For the simple score scheme with values {-m, ..., -1, 0, 1} occurring with probabilities {p_-m, ..., p_-1, p₀, p₁} we have,

K_- = (e^-λ* - e^-2λ*) E (Xe^λ*X).

We can set the left hand side of Equation (2) to some predetermined significance level, say P = 0.05 or 0.01, and solve for x. A segment with score exceeding $M_P=\frac{\ln n}{{\lambda }^{*}}+x$ is then said to be significant at the 100P% level.

In this paper, we use K_- in place of K* in Equation (2) for a "conservative" estimate of the probability and K₊ for a "generous" one.

We use Equation (2) with P = 0.05 and P = 0.01 to get M_0.05 and M_0.01 respectively. If the value of an excursion exceeds the critical value M_0.05 (or M_0.01), then the segment from the beginning of the excursion up to the base where the peak value is realized is said to be a high-scoring segment (HSS) significant at the 5% (or 1%) level.

HSS Selection

For each of the genomic sequences listed in Table 1, we obtain a set of HSS, significant at the 5% (or 1%) level. In each set of HSS, it is common to find several of them located close to one another. We thus apply a filtering procedure so that, if this happens, we shall only select one of several neighboring excursions as a representative for that part of the genome. In fact, we first sort all the HSS according to their aggregate scores. Starting with the one with the highest value, say segment A, we 'discard' neighboring HSS that are within 2 map units of it. After that, we pick among the rest (not including segment A and the discarded HSS), the HSS with the next highest value, say segment B, and repeat the process. Only the representative segments A, B, and so forth, will be used in replication origin prediction.

Results and Discussion

HSS Tables and Excursion Plots

Table 2 lists the HSS for each herpesvirus in Table 1. We have also tried locating high-scoring segments by running the excursions from the 3' end to 5' end of the genome. The results obtained are not much different from the "vanilla" version (i.e., from 5' to 3').

Table 2.

Herpesviruses : HSS at 5% level using the conservative bound.

HSS				HSS
Virus	Start	Peak	Value	Virus	Start	Peak	Value
alhv1	1204	1370	54	ebv	11854	11950	45
	32478	32850	48		77111	77150	24
	113630	113684	46		43158	43235	23
	85923	85992	45	ehv1	20348	20431	47
	72999	73115	44		134195	134276	36
	125691	125726	31		65055	65126	35
athv3	8827	8892	40		99301	99374	34
bohv1	100410	100484	26		11034	11141	32
	109702	109730	25		105796	105862	30
	128487	128515	25		73653	73746	27
	16593	16626	21		113818	113849	25
	113720	113738	18		149310	149341	25
	124479	124497	18		110314	110352	23
	29	45	16		128924	128992	23
	58542	58569	15	ehv2	160281	160518	102
bohv4	60687	60826	35		86522	86622	76
bohv5	68440	68507	49		53843	54012	61
	113549	113583	28		140661	140826	57
	129429	129463	28		4580	4655	51
	592	616	21		171454	171529	51
	86191	86215	21		95342	95440	50
	102074	102106	17		10772	10820	48
	92511	92535	15		39893	39977	48
	120935	120959	15		177646	177694	48
	59921	59938	14		113310	113399	47
	17408	17433	13		134709	134772	45
	41883	41899	13		166114	166207	42
calhv3	70131	70198	31		45831	45965	41
ccmv	50872	50973	50		15443	15482	39
	158344	158701	45		19722	19845	39
	95375	95603	39		182317	182356	39
	3519	3602	35		153977	154145	36
	24084	24156	33		123321	123362	35
	182982	183136	31		147222	147341	35
	14314	14370	23		34816	34884	29
	177170	177247	23		76380	76454	29
	189041	189075	22		103167	103223	29
	147310	147384	20		64344	64402	25
cehv1	116723	116836	53		786	831	24
	92092	92118	26	ehv4	109852	110086	60
	61680	61700	20		19878	19943	50
	132785	132805	20		132383	132462	49
	149415	149435	20		105284	105365	48
	52055	52075	17		23895	24016	43
	42984	43006	16		3984	4110	42
	11389	11407	15		73340	73509	37
	24415	24441	14		98849	98930	33
cehv15	11965	12011	28		46612	46674	32
	114927	114988	19		10630	10697	31
cehv16	92913	92940	23		58833	58906	31
	62970	62991	21		82616	82701	31
	133468	133489	21		127230	127351	31
	149813	149834	21		112929	112967	29
	8303	8331	20		145082	145120	29
	118685	118713	20	gahv1	24852	24890	30
	53056	53100	18	gahv2	106724	106811	35
	25423	25473	16	gahv3	11168	11198	27
	1717	1736	15		122384	122414	27
	114861	114890	15		134414	134461	26
	125280	125299	15		162999	163046	26
	30975	30991	14		58953	58999	25
cehv2	7681	7738	33	hcmv	3402	3542	41
	115791	115848	33		186855	186995	41
	61483	61503	20		16757	16915	35
	129527	129547	20		96685	96824	34
	144461	144481	20		11713	11808	32
	90857	90884	19		198116	198171	31
	51884	51910	14		173560	173599	30
	93873	93887	14		210724	210781	30
	112292	112320	14		26361	26475	27
cehv7	86167	86296	37		108222	108303	24
cehv8	149643	149720	33		159296	159380	24
	15671	15733	30		71011	71055	23
	29233	29278	29		226192	226230	23
	163766	163806	28
	177904	178092	28
	89538	89589	27
hcmv-m	3798	3939	42	mfrv	128046	128640	114
	181238	181334	33		23139	23374	109
	97069	97206	32		2488	3068	106
	173950	173994	32		32573	33752	84
	216020	216077	30		64296	64454	62
	203400	203456	29		111496	111624	44
	17082	17297	26		72739	72809	43
	12060	12145	25		53766	53825	32
	157590	157726	25		69912	70061	32
hhv6	130410	130501	59		114828	114860	32
	3605	3712	51	mmrv	2388	2967	111
	154838	154945	51		23902	24187	108
	137079	137210	43		33761	35136	103
hhv6b	132997	133163	62		130346	131085	97
	139482	139569	51		65611	65853	56
	3911	3988	37		74140	74204	37
	157232	157309	37		71311	71462	31
hhv7	134169	134376	117		117507	117551	29
	128589	128984	70		112930	113033	28
hhv8	136287	136704	93	muhv4	6000	6037	29
	982	1125	44	ohv2	115365	115545	72
	58833	58906	28		126823	127116	68
	23547	23598	27		118943	118988	42
	30712	30775	27		72630	72699	36
	119416	119467	27		1269	1370	29
	106412	106452	25		27589	27633	29
hsv1	62465	62485	20		76335	76370	26
	35000	35034	19		79158	79265	26
	115242	115303	19	oshv1	73292	73460	64
	131990	132008	18		35416	35493	61
	144115	144142	18		146021	146164	55
	11705	11734	17		190174	190312	54
	52753	52818	17		195928	196026	54
	96047	96069	16		201648	201786	54
	136146	136162	16		23065	23135	50
hsv2	5584	5628	35		161395	161505	50
	121621	121665	35		2682	2735	49
	52978	53003	19		180276	180329	49
	91716	91747	19		108068	108173	45
	146600	146631	19		171433	171549	44
	95238	95256	18		67872	67975	43
	48761	48778	17		114689	114763	42
	62919	62939	17	pshv1	18751	18791	31
	132691	132711	17		121452	121486	31
	81195	81220	16		160685	160719	31
	99337	99370	15		130332	130365	27
ichv1	6068	6290	81		151806	151839	27
	121738	121960	81		23896	23942	22
	104134	104399	70		134013	134049	21
	17065	17333	58		78233	78256	20
	132735	133003	58	rcmv	150923	151612	92
	451	726	50		207600	207980	80
	116121	116396	50		143617	144150	74
	60752	60845	30		178241	178326	37
	42919	43007	28		214638	214702	37
	20109	20187	24		219069	219153	33
	10016	10063	23		201767	201885	28
	125686	125733	23		161797	161929	27
mcmv	155163	156341	125		171828	171870	27
					24072	24108	21
	161228	161391	40	sahv2	28533	28613	45
	115543	115640	37	shv1	63862	63892	24
	102865	102960	35		96251	96275	21
	79497	79573	34		114686	114715	20
	15628	15724	33		129607	129636	20
	144170	144290	33		50382	50407	19
	73525	73579	27		75955	75984	17
	39209	39248	24		16151	16172	15
	92997	93036	24		33045	33063	15
	219239	219282	22		109083	109098	15
mehv1		NIL			135503	135518	15
					8432	8455	14
				thv	168842	168927	25
					24153	24200	23
					28257	28286	17
				vzv	2574	2785	39
					110195	110227	32
					119669	119701	32

Entries in italics are significant at 1% too.

For visualizing the locations of the selected HSS relative to the entire genome, the excursion plot is a convenient tool. The excursion plot of the Human Herpesvirus 3 (vzv) is presented in Figure 1, where the AT excursion values are plotted against the bases along the genome. The general appearance of Figure 1 is typical of the excursion plots for all the herpesviruses analyzed. In the case of vzv, three peaks with excursion values exceeding the 5% significance level are observed. Two of these peaks are close to the centers of the only two known replication origins of vzv (see Table 3).

Figure 1.

The Excursion Plot of the vzv virus. The horizontal line corresponds to the 5% significant level. The two triangles denote the locations of known replication origins of the vzv.

Table 3.

Prediction results at 5% level using the conservative bound.

Nearest HSS
Virus	Ori Center	Start	Peak	Value	Prediction
bohv1	111190	109702	109730	25	Yes
bohv1	127028	128487	128515	25	Yes
bohv4	97996.5	60687	60826	35	No
bohv5	113312	113549	113583	28	Yes
bohv5	129701	129429	129463	28	Yes
cehv1	61690.5	61680	61700	20	Yes
cehv1	61893.5	61680	61700	20	Yes
cehv1	132795.5	132785	132805	20	Yes
cehv1	132998.5	132785	132805	20	Yes
cehv1	149425.5	149415	149435	20	Yes
cehv1	149628.5	149415	149435	20	Yes
cehv16	62981	62970	62991	21	Yes
cehv16	133479	133468	133489	21	Yes
cehv16	149824	149813	149834	21	Yes
cehv2	61493.5	61483	61503	20	Yes
cehv2	129537.5	129527	129547	20	Yes
cehv2	144471.5	144461	144481	20	Yes
cehv7	109636.5	86167	86296	37	No
cehv7	118622.5	86167	86296	37	No
ebv	8313.5	11854	11950	45	No
ebv	40797	43158	43235	23	Yes
ebv	143825.5	77111	77150	24	No
ehv1	126262.5	128924	128992	23	Yes
ehv4	73909.5	73340	73509	37	Yes
ehv4	119471.5	112929	112967	29	No
ehv4	138577.5	132383	132462	49	No
gahv1	24871.5	24852	24890	30	Yes
hcmv	93923.5	96685	96824	34	Yes
hhv6	67805	130410	130501	59	No
hhv6b	69160.5	132997	133163	62	No
hhv7	66991.5	128589	128984	70	No
hsv1	62475	62465	62485	20	Yes
hsv1	131999	131990	132008	18	Yes
hsv1	146235	144115	144142	18	Yes
hsv2	62930	62919	62939	17	Yes
hsv2	132760	132691	132711	17	Yes
hsv2	148981	146600	146631	19	Yes
rcmv	77318	24072	24108	21	No
shv1	63878	63862	63892	24	Yes
shv1	114701	114686	114715	20	Yes
shv1	129901	129607	129636	20	Yes
vzv	110218.5	110195	110227	32	Yes
vzv	119678.5	119669	119701	32	Yes

For each replication origin, we list the high-scoring segment (at 5% level) closest to it. When the peak of a high-scoring segment is less than 2 map units away from the center of a replication origin, we say that our method has correctly predicted that particular replication origin.

Prediction Performance

The high-scoring segments are checked against known replication origins in herpesviruses to evaluate their performance as a prediction tool. Table 3 lists all the known replication origins for the herpesviruses in Table 1. These origins are reported either in published literature or GenBank annotations. For each replication origin, we list the HSS (at 5% level) closest to it. For this table we had used the "conservative" estimate for the value of K* (See Equations (2) and (3)). When the peak of an HSS is less than 2 map units (one map unit is one percent of the genome length) away from the center of a replication origin, we say that our method has correctly predicted that particular replication origin. From Table 3, we see that of the 43 replication origins known, compiled from literature or annotations, 32 of them are close to HSS that have been identified.

We had also tried using the "generous" estimate for K* at the 5% and 1% level of significance. Table 4 gives a summary of the performance of our prediction scheme when those bounds were used. The first two columns of the table gives the sensitivity level and positive prediction value of our scheme. Sensitivity refers to the percentage of replication origins predicted by our method, and PPV (positive predictive value) the proportion of HSS that correctly predict replication origins. APD (average predictive distance), given in map units (± one standard deviation), shows the average of the distances (in map units) between the center of each replication origin and the HSS that predicts it. Note that the APD values say that on average, when a prediction by an HSS is successful, the replication origin is about 0.35 map units away from it. We have also done some simple analysis of the location of the center of each replication origin with respect to the HSS closest to it. We count the number of times the center of replication origin falls within the left, right or center of the HSS. The columns %L, %R, and %C in Table 4 give these proportions. Our results show that the origin falls within the center of the HSS half the time.

Table 4.

Prediction Performance Summary.

Significance	Sensitivity	PPV	APD	%L	%R	%C
5% (C)	74%	22%	0.34 ± 0.57	16%	31%	53%
5% (G)	86%	17%	0.35 ± 0.53	24%	30%	46%
1% (C)	67%	25%	0.31 ± 0.52	14%	34%	52%
1% (G)	74%	18%	0.34 ± 0.57	16%	31%	53%

(C) indicates that the "Conservative" bound is used while (G) indicates that the "Generous" bound is used. Sensitivity refers to the percentage of replication origins predicted by our method, and PPV (positive predictive value) the proportion of HSS that correctly predict replication origins. APD (average predictive distance), given in map units (± one standard deviation), shows the average of the distances between the center of each replication origin and a HSS that predicts it in map units. %L, %R and %C count the number of times the center of replication origin falls within the left, right or center of the HSS.

Comparison with Other Approaches

How does the AT excursion method compare with the sliding window approach using palindrome based scoring schemes previously presented in [12]? Since the BWS₁ scheme has been shown to perform best among the various palindrome based schemes, we have examined the numbers of replication origins correctly predicted by AT excursion and by BWS₁. The results are summarized in Figure 2.

Figure 2.

Predictions of AT excursion and BWS₁. In this figure, the set A consists of origin replications predicted by the AT excursion method and B consists of those predicted by the BWS₁ method. A ⋂ B^C = {cehv7₁, cehv7₂, ehv4₁, hsv2₁, hsv2₂, hsv2₃}, A^C ⋂ B = {cehv16₂, cehv16₃, ebv₁, ebv₃, hhv6, hhv6b, rcmv}, (A ⋃ B)^C = {bohv4, ehv4₂, ehv4₃, hhv7}. The rest of the replication origins (26 of them) are predicted by both methods. Note that for viruses with several known replication origins, such as the hsv2, which has three (see Table 3), we denote the replication origins as hsv2₁, hsv2₂, hsv2₃, etc.

The majority of the 43 known origins in the herpesviruses listed in Table 1 are predicted by both methods and most of the remaining ones are predicted by one method or the other. Only four of the origins fail to be predicted by either method. This suggests that the AT excursion method and the BWS₁ scheme complement each other very well.

There are certain advantages in the AT excursion approach over BWS₁. First, AT excursion does not require any sequence specific parameters to be prescribed by the user. It is window size free because it does not require any sliding window to measure AT concentration. Moreover, while the palindrome based methods require the specification of a minimal palindrome length before the analysis can be carried out, no such parameter is needed for AT excursion. Second, the AT excursion method is statistically based, as the probabilistic distribution has already been established [20-22]. This allows the statistical significance for HSS be evaluated easily.

We also note that the more elaborate AT excursion approach performs better than the simpler procedure of measuring the percentage of A and T bases on a sliding window in terms of number of correct predictions and the proximity of these predictions to the true origins. Out of the 43 known replication origins for the herpesviruses in Table 1, 32 are correctly predicted by AT excursion but only 28 by AT sliding window plot. Furthermore, the boxplots of the predictive distances (Figure 3) of the AT excursion approach suggests that the predictions given by the AT excursion approach are much closer to known replication origins as compared to those of the AT sliding window plot approach. (In fact, the predictive distances of the AT excursion approach compared to that of the PLS and BWS₁ approaches mentioned in [12] are observably shorter. See Figure 3.) This suggests that the excursion values might more correctly capture the essence of A/T abundance variation along genomic sequences.

Figure 3.

Predictive Distances for PLS, BWS₁, AT-swp and AT excursion. These boxplots show the predictive distances for PLS, BWS₁, AT-swp and AT excursion.

Herpesvirus Replication Origins Alignment and Motif Finding

One might ask whether or not the nucleotide sequences around replication origins in various viruses of the same family share sufficient similarities so that the origins can be identified by sequence alignments and motif finding techniques. We therefore extracted the nucleotide sequences of the known herpesvirus origins according to their documented locations for closer examination. These sequences are available as supplementary materials on the companion website. A multiple alignment using CLUSTAL W [24] and motif searches using MEME and MAST [25,26] have been conducted for the herpesvirus origin sequences. No significant sequence similarity or common motif pattern across all the origin sequences has been found, agreeing with the findings of [11,13,14].

What if we first classify these nucleotide sequences according to some classification schemes, will the members within each class share noticeable sequence similarities? We classified the origins according to (i) the sub-family of the virus (herpesviruses are classified into the alpha, beta, and gamma sub-families by their biological properties [27]), (ii) the type of origin (i.e., whether the origin is a oriL, oriLyt or oriS). We ran MEME and MAST separately on the sequences in each sub-family/type of origins to detect common motif patterns. From the outputs under classification (i), we note that the origins from the alpha sub-family can be further divided into two groups. Each group has a common motif pattern across its members. For the beta and gamma sub-families, no distinct patterns can be found. However, the rcmv and ebv origins contain many repeat patterns. For classification (ii), we find that both the oriL and oriLyt origins contain sequence motifs common to a number of their members. No motif was found for oriS sequences. The results of our motif search are made available in the supplementary materials.

Although our investigations are preliminary, the motifs found in these subsets of herpesvirus genomes may suggest new information that can be incorporated into the replication origin prediction procedures.

Other Families of Viruses

Aside from the herpesviruses, we have also applied the AT excursion method to search for HSS in the poxviruses and iridoviruses. These two viral families are chosen because, like the herpesviruses, they are large, complex dsDNA viruses with no RNA stage. Their genome lengths are also similar in magnitude to those of the herpesviruses.

Poxviruses infect a large variety of animal species that gather in swarms and herds (e.g., mosquitoes, cows). Smallpox is a major disease caused by the variola virus, a member of the poxvirus family. Smallpox was eradicated in 1977 by preventive inoculations with cowpox or vaccinia viruses through the dedicated efforts of the World Health Organization and many individuals. In the recent few years, as the threat of the variola virus being used as a biological weapon is raised, there is growing interest in further studying poxviruses for biodefense purposes [28,29]. Iridoviruses are found in a variety of fish, amphibians, and reptiles. Some iridoviruses have been associated with serious diseases (e.g., viral erythrocytic necrosis of salmonids), while others have only been found in apparently healthy animals (e.g., goldfish iridovirus). Iridovirus infection is considered a serious concern in modern aquaculture, fish farming, and wildlife conservation [30].

Amongst these two families, only one genome, namely the Chilo iridescent virus, has documented replication origin locations [31]. Our method has correctly predicted one of these locations. Due to the lack of confirmed origin locations, prediction accuracy cannot be tested on these families. Nevertheless, our predictions may assist researchers to investigate these viruses experimentally to identify and confirm the exact locations of replication origins in their genomes. We have, therefore, made our prediction results available at [1].

AT excursion applied to larger genomes

To gauge whether the AT excursion approach can potentially be generalized to predict replication origins for non-viral genomes, we apply it to several archaeal and bacterial genomes which have been previously analyzed. From [4,5,32] we are able to compile a list of 15 known or suggested replication origins (11 known, 4 suggested). Using the AT excursion method, we manage to correctly predict 9 of the replication origins (6 known, 3 suggested). Although our studies are preliminary, the results show that the AT excursion method can work reasonably well even on larger genomes.

Conclusion

This paper introduces the AT excursion method to quantify local AT abundance in genomic sequences. The simple and intuitive idea of locating regions with high AT content as potential replication origin sites proves to be effective in identifying several replication origins not previously predicted. This shows that the AT excursion approach is a valuable addition to existing prediction tools. However, we have also observed that quite a number of the statistically significant HSS found by AT excursions are not close to replication origins. Whether these HSS correspond to other important functional sites in the genomic sequences remains an interesting question to be investigated.

The availability of statistical significance criteria and the independence of ad hoc parameters like the minimal palindrome length and sliding window size make the AT excursion method particularly easy to apply to those viral genomes where no replication origin information in similar and related genomes is available. On the other hand, if such information is available, the AT excursion method is not capable of taking advantage of it. To address this issue, machine learning approaches (e.g., neural networks and support vector machines), which better allow us to use knowledge in related genomes, are currently being explored. We anticipate that a combination of score based statistics with machine learning approaches will provide a highly accurate prediction tool set for replication origins.

Authors' contributions

DC participated in the design of the study and performed the data and statistical analysis. KPC and MYL conceived the study, and participated in its design and coordination. All authors contributed to writing, reading and approving the final manuscript.