Open Access

Sorting by reversals and block-interchanges with various weight assignments

BMC Bioinformatics200910:398

https://doi.org/10.1186/1471-2105-10-398

Received: 3 August 2009

Accepted: 4 December 2009

Published: 4 December 2009

Abstract

Background

A classical problem in studying genome rearrangements is understanding the series of rearrangement events involved in transforming one genome into another in accordance with the parsimonious principle when two genomes with the same set of genes differ in gene order. The most studied event is the reversal, but an increasing number of reports have considered reversals along with other genome rearrangement events. Some recent studies have investigated the use of reversals and block-interchanges simultaneously with a weight proportion of 1:2. However, there has been less progress towards exploring additional combinations of weights.

Results

In this paper, we present several approaches to examine genome rearrangement problems by considering reversals and block-interchanges together using various weight assignments. An exact algorithm for the weight proportion of 1:2 is developed, and then, its idea is extended to design approximation algorithms for other weight assignments. The results of our simulations suggest that the performance of our approximation algorithm is superior to its theoretical expectation.

Conclusion

If the weight of reversals is no more than that of block-interchanges, our algorithm provides an acceptable solution for the transformation of two permutations. Nevertheless whether there are more tractable results for studying the two events remains open.

Background

In comparative genomics, the study of genome rearrangements has been one of the most promising methods for tracing the evolutionary history using gene order comparisons between organisms. The mathematical model simply treats a chromosome in the genome as a permutation of integers, where each integer represents a gene. Specifically, these integers are associated with signs, + or -, to indicate the corresponding orientation (strandedness) of the gene. A basic task in genome rearrangement studies is to economically transform one permutation into another using restricted types of global mutations. Compared with local (point) mutations, global mutations are rare, but can provide valuable clues about the evolutionary history of organisms.

The most widely studied type of global mutations is the reversal (also called inversion) which inverts a segment in the permutation and changes the sign of each integer in that segment. If we only consider reversals, the so-called problem of sorting by reversals (SBR) is to find the shortest series composed of reversals that transforms the given permutation into another, where the minimum number of reversals is often regarded as the (reversal) distance between two permutations. SBR is a well-studied subject in computational biology, and its first polynomial-time algorithm was proposed by Hannenhalli and Pevzner in 1995 [1]. Other groups have subsequently simplified and improved this algorithm [25]. To date, the best running time of an algorithm for SBR is O(n3/2) in theoretical analysis, as presented by Han [6]. It remains unclear whether SBR can be solved in O(n log n) time, but a plausible answer was recently given by Swenson et al. [7], providing two new algorithms; the first runs in randomized O(n log n) time, whereas the other is a deterministic algorithm with running time O(n log n + kn), where k is a data-dependent parameter and both its average and standard deviation are small constants derived from extensive experiments [7]. Moreover, a linear-time cost is sufficient to compute the reversal distance [8].

In addition to reversals, transpositions and block-interchanges are also global mutations that act on a permutation. The former exchanges two adjacent segments, and the latter is a generalization of a transposition in which exchanged segments do not have to be adjacent. The problem of transpositions is called sorting by transpositions (SBT), in which the minimum number of transpositions required to complete the transformation is sought. Currently, we know nothing about its complexity, but several approximation algorithms have been proposed [911]. However, the problem of sorting by block-interchanges (SBBI) using block-interchanges only is tractable and was first studied by Christie [12] using the graph approach and then by Lin et al. [13] using the algebraic formalism. Recently, Feng and Zhu [14] introduced a new data structure to improve the approximation and exact algorithms for SBT and SBBI, respectively, to achieve the time complexity O(n log n).

Considering reversals and transpositions together leads to the problem of sorting by reversals and transpositions (SBR+T), i.e., it allows one to perform reversals and transpositions alternatively during the transforming process. Because of the two operations used, we assign weights w r to reversals and w t to transpositions, and thus seek a transforming series with a minimum sum of weights. For w r : w t = 1 : 1, Lin and Xue [15] and Walter et al. [16] presented approximation algorithms with a factor of 2. By incorporating inverted transposition, which inverts one of two swapped segments of a transposition and usually has equal weight w it to w t , in the transformation, 2-approximation algorithms have been reported by two groups [15, 17]. Furthermore, Eriksen [18] developed a (1 + ε)-approximation algorithm for the weighted assignment of w r : w t (w it ) = 1 : 2. Bader and Ohlebusch [19] recently devised a 1.5-approximation algorithm with time O(n2) for any weight proportion of w r : w t (w it ) between 1 : 1 and 1 : 2. Nevertheless, it remains unknown whether tractable results can be derived for SBR+T.

In contrast, studying the block-interchanges (with each weight w bi ) along with reversals seems easier, i.e., the problem of sorting by reversals and block-interchanges (SBR+BI). For w r : w bi = 1 : 2, three groups of researcheres began from different perspectives but all achieved tractable results for SBR+BI [2022]. Yancopoulos et al. [20] introduced a universal double-cut-and-join operation that accounts for reversals, translocations, fissions, fusions and block-interchanges by assigning a weight of 2 to block-interchanges and 1 to others. With a slight modification to their algorithm, one can optimally solve SBR+BI [21]. In addition, the approach of Lin et al. [21] based on the so-called breakpoint graph[1], whereas Mira and Meidanis [22] adopted the algebraic viewpoint by introducing the parameter norm to represent the weight of a rearrangement event. By adding a number of local mutations, Bader [23] tackled the problem of unequal gene content using a heuristic algorithm. Despite tractable results when studying SBR+BI under w r : w bi = 1 : 2, to our knowledge, this is the only type of weight assignments that have been considered so far. In this paper, we study genome rearrangement problems by considering reversals and block-interchanges simultaneously using various weight assignments.

On the other hand, a traditional yet effective way to approach a complex problem is to devise an approximate solution that is "not too far from" the exact solution. Approximation algorithms are, indeed, a well-developed branch of the computer sciences [24]. A β-approximation algorithm (β > 1) for a minimization problem runs in time polynomial to the input size and returns a feasible solution having a quality value that is, at most, β times the optimum. More interestingly, since the factor β is obtained from the worst-case analysis, an approximation algorithm with a higher factor does not imply poor average performance. To address genome rearrangement problems, two approximation algorithms are developed in this work, together with theoretical analyses and experiments to evaluate their performance.

Methods

Preliminaries

A signed linear permutation is a permutation of {1, 2, ..., n}, where each element is labeled by + or - to indicate the orientation of its corresponding gene. A reversal r(i, j) (with 1 ≤ ijn) is an operation that inverts the order of elements in a segment of by transforming into . Another operation, block-interchange bi(i, j, k, l) (with 1 ≤ ij < kln), exchanges two non-intersecting segments ( ) and by converting to . For the two operations considered in our study, the weights of reversals and block-interchanges are denoted by w r and w bi , respectively.

Given two permutations and , the WGRP(w r , w bi ), abbreviated from Weighted Genome Rearrangement Problem with w r and w bi , is used to find a minimum weighted sequence of reversals and block-interchanges for transforming into , and its sum of weights is regarded as the distance between and . In general, the problem is simplified as follows. First, the elements in and are relabeled such that becomes the identity permutation = (1, 2, ..., n), and therefore the transformation from to is similar to a sorting process. The distance is also simplified as dist( ). Next, for w r > 0, we replace w bi with w bi /w r and fix w r to 1.

When dealing with the signed permutation of size n, most studies extend and transform into an unsigned mapping π = (π0, π1, ..., π2n+1) of {0, 1, ..., 2n + 1} beforehand by replacing each positive element x of by 2x - 1 and 2x, each negative element -x by 2x and 2x - 1, and adding two elements π0 = 0 and π2n+1= 2n + 1. For example, if = (2, -5, -3, -4, -6, 7, 1), then its unsigned mapping is π = (0, 3, 4, 10, 9, 6, 5, 8, 7, 12, 11, 13, 14, 1, 2, 15). Each operation on also corresponds to a specific operation on π as follows: A reversal of the form r(2i + 1, 2j) is said to be legal for π since it mimics the reversal r(i + 1, j) on [1], and similarly a block-interchange bi(2i + 1, 2j, 2k + 1, 2l) is legal on π since it acts like the block-interchange bi(i + 1, j, k + 1, l) on . Considering the above as an example, the reversal r(5, 12) and block-interchange bi(1, 8, 11, 14) are legal, whereas r(3, 5) and bi(1, 9, 11, 14) are not. Furthermore, performing r(5, 12) (resp. bi(1, 8, 11, 14)) on π is equivalent to performing r(3, 6) (resp. bi(1, 4, 6, 7)) on . In other words, the WGRP(w r , w bi ) between and can be solved by computing a minimum weighted sequence of legal reversals and block-interchanges for converting π to I. We hereafter use π and I instead of and , and legal reversals and block-interchanges in our algorithms.

Breakpoint graph

Let π be the permutation mentioned previously. The so-called breakpoint graph BP(π) is a powerful analysis tool for studying genome rearrangement problems, and is defined as an edge-colored graph with 2n + 2 vertices as follows: For 0 ≤ in, π2iconnects to π2i+1by a black edge and 2i is joined to 2i + 1 by a gray edge (Figure 1). In BP(π), a gray edge (π i , π j ) is said to be oriented if i + j is even, and otherwise it is unoriented. A cycle is said to be alternating if it contains alternating black and gray edges. Since the degree of each vertex is 2 (a black edge and a gray edge), the graph BP(π) can be uniquely decomposed into edge-disjoint and alternating cycles. In addition, a cycle is oriented as long as it has an oriented gray edge, otherwise, it is unoriented. The length of a cycle is the number of black (or equivalently, gray) edges it contains. We use l-cycle to denote an alternating cycle with length l, and c(π) to denote the number of cycles in BP(π), e.g., in Figure 1, c(π) = 2: one is a 5-cycle and the other is a 3-cycle. Note that c(π) = n + 1 if and only if π = I.
Figure 1

The breakpoint graph BP ( π ) of the permutation π , in which black edges are represented as solid lines and gray edges as dashed lines. The gray edge (4, 5) is oriented whereas (2, 3) is unoriented. In addition, there are two components C1 and C2, in which the former is a hurdle.

Each gray edge g = (π i , π j ) is associated with the interval < i, j >, and two gray edges overlap if their corresponding intervals overlap but neither of them properly contains the other. Moreover, two cycles overlap if their gray edges overlap, and a set of overlapping cycles forms a component. As with oriented cycles, a component is oriented if at least one of its cycles is oriented, and it is unoriented otherwise. Using the result of Bader et al. [8], the oriented and unoriented components can be efficiently determined in linear time.

A complex and interesting component of the Hannenhalli and Pevzner (HP) theory copes with the hurdle, which currently has several slightly different definitions [1, 2, 18, 25, 26]. Here we adopt a similar statement to the work of Eriksen [18] but with linear permutations. A hurdle H is an unoriented component such that there is an interval containing all vertices in H but no vertices in other unoriented components. Here we allow continuous intervals by setting 0 to be the successor of 2n + 1. For the permutation π in Figure 1, C1 is a hurdle since < 12, 15 > < 0, 1 > is an interval containing the unoriented component C1 only. Although < 2, 11 > contains C2 only, C2 is not a hurdle since it is an oriented component. As a result, the number of hurdles of π in Figure 1 is one, i.e., h(π) = 1.

The HP theory shows that the variations in c(π) and h(π) guide the transformation between two permutations. For an arbitrary operation ρ acting on π, let Δc ρ = c(ρ·π) - c(π) and Δh ρ = h(ρ·π) - h(π). For convenience, we further abbreviate Δc ρ (resp. Δh ρ ) to Δc r (resp. Δh r ) if ρ is a reversal and to Δc bi (resp. Δh bi ) if ρ is a block-interchange. HP showed that Δc r ≤ 1 and Δh r ≤ 2 [1]. Christie presented that Δc bi ≤ 2 but on unsigned permutations [12]. A similar argument as Christie's work [12] can extend the upper bound of Δc bi on signed permutations.

Lemma 1 For every permutation π and block-interchange bi, Δc bi ≤ 2.

Proof: A block-interchange exchanges two non-overlapping segments, whereas a segment can be specified by two black edges. Let V bi be the set of vertices connected by the black edges for determining the block-interchange bi, and c(V bi ) be the number of cycles containing the vertices in V bi . For example in Figure 2a, V bi = {a, d, e, b, c, f} and c(V bi ) = 1. According to the number of black edges containing vertices in V bi , we have the following two cases:
Figure 2

The block-interchange bi defined by (a) three black edges increases the number of cycles by two, whereas (b) four black edges decreases the number of cycles by two. The pair of blue parentheses specifies one of two exchanged segments of bi, and the small dotted lines denote alternating paths.

CASE1: Three black edges. Applying bi to π affects only the cycles whose vertices are in V bi . Due to the three black edges in this case, we have 1 ≤ c(V bi ) ≤ 3 and the same is true after applying bi, implying that Δc bi ≤ 2 (Figure 2a).

CASE2: Four black edges. A similar statement as CASE1 shows that Δc bi ≤ 3 as a result of 1 ≤ c(V bi ) ≤ 4. The only possibility in which Δc bi = 3 comes from the result of breaking the cycle in π into four cycles in bi·π, but it cannot happen with the subsequent argument. As shown in Figure 2b, the block-interchange bi* with c(Vbi*) = 4 results in c(Vbi*) = 2 after performing bi*, and hence, Δcbi*≠ 1 - 4 = -3. However, if there is a bi such that Δc bi = 3, then the vertices of V bi will be in four cycles of BP(bi·π). Then the bi* exchanging the two swapped segments of bi has Δc bi * = -3 when it acts on bi·π, a contradiction. Consequently, Δc bi ≤ 2.   □

WGRP(w r = 1, w bi = 2)

For a sorting series S = ρ1, ρ2, ..., ρ t transforming π into I, where ρ i represents either a reversal or a block-interchange, let the number of reversals be d r (S) and the number of block-interchanges be d bi (S). Thus, the weighted sum of S is d(S) = w r ·d r (S) + w bi ·d bi (S). The distance dist(π) is then the minimum d(S) among all sorting series S of converting π to I. First, we set w bi = 2 and consider WGRP (1, 2). Lemma 2 gives a lower bound of dist(π) in a more general case when 2 ≤ w bi .

Lemma 2 dist(π) ≥ n + 1 - c(π) for WGRP(1, w bi ) with 2 ≤ w bi .

Proof: Since Δc r ≤ 1 and Δc bi ≤ 2, an operation increasing the number of cycles by one costs at least , which equals 1 in the case of w r = 1 and 2 ≤ w bi . However, in the best situation, there are at least n + 1 -c(π) cycles to be increased because of n + 1 cycles in BP(I). As a result, the cost of any transformation from π to I is at least n + 1 -c(π) for WGRP(1, w bi ) with 2 ≤ w bi .   □

To deal with WGRP(1, 2), Lemma 2 shows that if the rearrangement sequences for sorting π are composed of reversals with Δc r = 1 and block-interchanges with Δc bi = 2, the cost of such a sequence is equal to the lower bound of dist(π), and hence is optimal. The strategy for selecting best reversals and block-interchanges is the core of the algorithm proposed by Lin et al. [21]. Their algorithm distinguished between oriented and unoriented components, and then sorted them separately, i.e., used the algorithm of Kaplan et al. [2] to sort all oriented components and the algorithm of Lin et al. [13] to deal with the unoriented components. Here we also utilize a known algorithm for SBR, called ASBR, to tackle oriented components but we modify the method for sorting unoriented components using the following theorem.

Theorem 1 Let g = (π i , π k ) and f = (π j , π l ) be unoriented gray edges of a component. If g and f overlap, then there is a block-interchange with Δc bi = 2 in this component.

Proof: WLOG, we assume that i and l are even and j and k are odd with i < j < k < l (other cases of i, j, k and l can be illustrated similarly). According to the number of cycles containing g and f, there are two main cases:

CASE1: g and f are in the same cycle. We further consider two subcases according to whether π i and π j are connected by a black edge:
  1. (1)

    j = i + 1, i.e., there is a black edge linking π i and π j (Figure 3a). Using the assumption of k < l, and that k is odd and l is even, there is no black edge between π k and π l . Therefore, we use the three black edges, (π i , π j ), (a, π k ), and (π l , b) to determine the block-interchange bi(j, k - 1, k, l). After performing it, the number of cycles is increased by two (Figure 3a), i.e., Δc bi = 2.

     
Figure 3

Two unoriented gray edges g = ( π i , π k ) and f = ( π j , π l ) overlapping in a component are in the same cycle with (a) j = i + 1 and (b) j > i + 1, whereas (c) g and f are in different cycles.

  1. (2)

    j > i + 1. Let V bi = {π i , a, b, π j , c, π k , π l , d (Figure 3b). There are no alternating paths from vertex a to c without passing a vertex in Vbi\{a, c} since g and f are in the same cycle. Consequently, one of the two cases of alternating paths linking vertices a, b, c, and d is demonstrated in Figure 3b. In this case, let the block-interchange be bi(i + 1, j - 1, k, l) and thus, in BP(bi(i + 1, j -1, k, lπ) the four vertices, a, b, c, and d, belong to one cycle. (The other case can be similarly demonstrated.) We have c(bi(i + 1, j -1, k, lπ) = c(π) + 2, which implies that Δc bi = 2.

     

CASE2: g and f are in two different cycles (Figure 3c). Recall that the order and positions of i, j, k, and l are fixed via the assumption. On the condition that g and f are parts of different cycles, π i and π j are never joined by a black edge. In addition, the vertex a connects to b (or d) by an alternating path that will result in the subcase (2) of CASE1. As a consequence, Figure 3c is the unique possibility in this case, and performing the block-interchange bi(i + 1, j - 1, k, l) leads to Δc bi = 4 - 2 = 2.   □

All gray edges are unoriented in unoriented components by definition, and furthermore, HP theory presents that for every gray edge g not in a 1-cycle, there is another gray edge f that overlaps with g[1]. In other words, it is always feasible to find two unoriented gray edges overlapping in unoriented components. By repeatedly applying the block-interchanges constructed in Theorem 1, all unoriented components are eventually sorted. We summarize the procedures as AWGRP(1,2) as follows:

Algorithm for WGRP(w r = 1, w bi = 2) (AWGRP(1,2))

Input: A signed permutation .

Output: A sorting series composed of reversals and block-interchanges for optimally transforming into .

1: Transform into its unsigned mapping π and construct BP(π);

2: Use the algorithm developed by Bader et al. [8] to distinguish between oriented and unoriented components;

3: Perform the algorithm of Han [6] to sort all oriented components;

4: Repeatedly apply the block-interchanges constructed by Theorem 1 to sort all unoriented components;

5: Mimic the sorting series of π to I to the transformation between and ;

In AWGRP(1,2), Step1 and Step2 cost linear time, while Step5 can be implemented in O(n log n) time [14, 27]. Recently, Feng and Zhu [14] developed a new data structure, called the permutation tree, to improve certain algorithms for SBT and SBBI, to achieve the time complexity O(n log n). This group used the permutation tree to implement two core procedures, Query and Transposition, which were developed by Hartman and Shamir [10] on the breakpoint graph. The former is used to find a pair of black edges intersecting the given pair of black edges, and the latter is used to adjust the data structures after applying transpositions. Although the term "intersecting" is defined on black edges [10], it is indeed the same concept as "overlap" here, and thus, can be used to find two overlapping unoriented gray edges to piece together block-interchanges. Moreover, since a block-interchange can be mimicked by two transpositions, a slight modification of the Transposition procedure [10] can be applied to retain the structures after performing block-interchanges. In short, the method of Feng and Zhu [14] to enhance the algorithm of Hartman and Shamir [10] can also be extended to cope with performing block-interchanges on unoriented components in Step4, for which we do not give a detailed description here. Accordingly, Step4 costs O(n log n) time. The running time of Step3 is O(n3/2) in a theoretical analysis [6], which is currently the best, or O(n log n) in most cases [7], depending on which algorithm is used to address SBR. As a result, theoretically, the total time complexity of AWGRP(1,2) is O(n3/2).

WGRP(w r = 1, 2 < w bi < 3)

In this subsection, we adjust the weight of block-interchanges to 2 < w bi < 3 and investigate WGRP(1, 2 < w bi < 3). A lower bound of n + 1 c(π) for dist(π) is given in Lemma 2, and on the other hand, taking the parameters Δh r and Δh bi into account can establish another lower bound. Let Δ(c-h) r = Δc r - Δh r and Δ(c - h) bi = Δc bi - Δh bi . We know that Δh r ≤ 2 and Δ(c - h) r ≤ 1 from the literature [1], and subsequent work is required to obtain a lower bound of Δh bi for bounding Δ(c - h) bi .

Let bi be a block-interchange and V bi be the set of vertices connected to the black edges of bi. If a hurdle H has no vertices of V bi in its interval H , then after performing bi, H still contains all vertices of H but no vertices in other unoriented components, i.e., H will be unchanged in BP(bi·π). This provides that Δh bi ≥ -h(V bi ), where h(V bi ) is the number of hurdles including vertices of V bi , since there are h(V bi ) hurdles whose intervals contain the elements in V bi and performing bi removes h(V bi ) hurdles at most. By using the bound for Δh bi , Lemma 3 immediately derives an upper bound for Δ(c - h) bi .

Lemma 3 For every permutation and block-interchange bi, Δ(c - h) bi ≤ 3.

Proof: Let c a (V bi ) be the number of cycles containing vertices of V bi after performing bi. Clearly, c(V bi ), c a (V bi ) {1, 2, 3, 4} and recall that c a (V bi ) - c(V bi ) = c(bi·π) - c(π) ≤ 2. We prove this lemma by first considering the achievable situations of c(V bi ) = 4 and c a (V bi ) = 4. Lemma 1 demonstrates that the only possibility for c a (V bi ) = 4 is Δc bi = 4 - 2 = 2, in which the two cycles including vertices of V bi belong to a component. Consequently, Δh bi ≥ -h(V bi ) ≥ -1, and then Δ(c - h) bi ≤ 2 - (-1) = 3. Using a similar argument, another case of c(V bi ) = 4 has Δc bi = 2 - 4 = -2 and h(V bi ) ≤ c(V bi ), indicating that Δ(c - h) bi ≤ -2 - (-4) = 2. Both cases satisfy this lemma.

Next, consider that c(V bi ), c a (V bi ) {1, 2, 3} is sufficient to show the remaining instances. In these cases, we have Δh bi ≥ -h(V bi ) ≥ -c(V bi ), and thus Δ(c - h) bi ≤ (c a (V bi ) - c(V bi )) - (-c(V bi )) = c a (V bi ) ≤ 3. This completes the proof.   □

Next, from Lemma 3, we compute another lower bound for dist(π). HP proved that one must decrease dist r (π) = n + 1 - (c(π) - h(π) - f(π)) to 0 to complete the sorting process if only reversals are allowed, where f(π) is the characteristic function for the existence of a fortress, i.e., f(π) is 1 if π is a fortress and 0 otherwise. In addition, by using a similar argument as Lemma 2, since Δ(c - h) r ≤ 1 and Δ(c - h) bi ≤ 3, an operation of increasing c(π) - h(π) by one costs at least min , which equals when 2 < w bi < 3. There are, however, at least n + 1 - c(π) + h(π) to be increased, leading to a lower bound for dist(π) in the following lemma.

Lemma 4 dist(π) ≥ (n + 1 c(π) + h(π)) for WGRP(1, 2 < w bi < 3).

After obtaining two lower bounds of dist(π), we can evaluate the approximation ratios of two proposed algorithms, AWGRP(1,2) and ASBR, as they are employed to solve WGRP(1, 2 < w bi < 3), where ASBR is an algorithm used to optimally solve SBR.

Theorem 2 ASBR is an approximation algorithm for WGRP(1, 2 < w bi < 3) with a ratio close to .

Proof: The sorting series given by ASBR comprises dist r (π) reversals and therefore, to be an approximation algorithm for WGRP(1, 2 < w bi < 3), ASBR has the factor close to   □

In Theorem 2, we bypass the effect of f(π) for two reasons: First, the probability that a random signed permutation of size n contains a fortress is Θ(n-15), which is extremely rare [26]. Second, HP illustrated the concept of fortress with a permutation π having dist r (π) = 23 + 1 - 12 + 3 + 1 = 16 [1], which is, in fact, the minimal dist r (π) for a permutation being a fortress. In other words, for f (π) = 1, the ratio is at most when 2 < w bi < 3, which is nearly .

Theorem 3 AWGRP(1,2) is a -approximation algorithm for WGRP(1, 2 < w bi < 3).

Proof: For sorting a permutation π with only oriented components, HP presented that ϕ(π) = b(π) - c(π) reversals are sufficient, where b(π) is the number of black edges in π. More specifically, for sorting an oriented component , we need reversals, in which b( ) (resp. c( )) is the number of black edges (resp. cycles) in . Similarly, if sorting a set of oriented components, an ASBR will produce reversals, which is also the same in AWGRP(1,2). When dealing with a set of unoriented components, AWGRP(1,2) constructs block-interchanges since each decreases by two.

To convert π to I, AWGRP(1,2) outputs a sorting series with weight sum , and a lower bound of dist(π) is ϕ(π) = n + 1 - c(π) by Lemma 2. As a result, AWGRP(1,2) is an approximation algorithm for solving WGRP(1, 2 < w bi < 3) with the factor given by   □

Theorems 2 and 3 give the approximation ratios of ASBR and AWGRP(1,2), respectively, for approaching WGRP(1, 2 < w bi < 3), where their ratios are both at most 1.5. By always selecting the better result of AWGRP(1,2) and ASBR, we receive a smaller ratio of , whose maximum is /2 ≈ 1.225 when the two terms coincide.

WGRP(w r = 1, 1 ≤ w bi < 2)

In the sequel, we readjust the weight of block-interchanges to 1 ≤ w bi < 2 and examine WGRP(1, 1 ≤ w bi < 2). Two lower bounds mentioned above, (n + 1 - c(π) + h(π)) and ϕ(π), are not proper here since the former is too small and the latter is no longer correct. A concise way to obtain a feasible lower bound is to take all oriented components in π as unoriented ones. Owing to the increase of at most two cycles by a block-interchange, a lower bound of dist(π) for WGRP(1, 0 < w bi < 2) is .

With the bound, then we have the following theorem.

Theorem 4 AWGRP(1,2) is a -approximation algorithm for WGRP(1, 0 < w bi < 2).

Proof: Recall that AWGRP(1,2) produces a sorting series with ϕ( ) reversals and block-interchanges. Consequently, to be an approximation algorithm for WGRP(1, 0 < w bi < 2), AWGRP(1,2) has the factor of   □

Since reversals are main mutations from the evolutionary viewpoint, its weight is often no more than weights of other mutations. Therefore, we focus on improving the algorithm to efficiently cope with WGRP(1, 1 ≤ w bi < 2).

We first observed the variation of the approximation ratio in Theorem 4. When w bi is close to 1, the factor approaches 2, which is insufficient to be used in practice. There are two ways to approach this inefficiency. The first is to make the lower bound higher by considering the fact that block-interchanges do not remove oriented components, and thus, an oriented component has at least one reversal to sort it. However, this does not indicate that is a new lower bound for k oriented components contained in π, since an operation may merge most of the oriented components into a single one. Figure 4 is an example of this, and this type of operations may result in the overestimate of becoming a lower bound. Therefore, we slightly enhance the lower bound by considering that if there is a permutation π whose BP(π) contains an oriented component, then , where the result of ϕ(π) - 1 is caused by an optimal reversal.
Figure 4

The illustrated block-interchange merges four oriented components into one at a time.

Next, we improve the algorithm by adding a new component. When 1 ≤ w bi < 2, the block-interchange is superior to the reversal since the former decreases ϕ(π) by at most two whereas the latter decreases it by at most one. Therefore, a straightforward idea is to use optimal block-interchanges whenever possible. Theorem 1 says that if two gray edges are unoriented and overlapping, then the corresponding block-interchange has Δc bi = 2, which is true regardless of oriented or unoriented components. Nevertheless, there may be no gray edges to satisfy the conditions of Theorem 1 in oriented components. Whenever there are no gray edges to form a block-interchange, we adapt a heuristic method to choose the oriented gray edge oge with maximum P(oge) = N(ooge) - N(ouge), where N(ooge) and N(ouge) are the number of oriented and unoriented gray edges overlapping with oge, respectively.

Let oge = (π i , π j ) be an oriented gray edge, and r oge be a reversal defined by two black edges linking π i and π j . Then, we immediately know that i + j is even, and hence, both i and j are either even or odd. The reversal r oge , irrespective of "even" or "odd" case, results in breaking a cycle into two smaller ones, i.e., = 1, as demonstrated in Figure 5. Notice that an oge can correspond to a reversal having Δc r = 1, and it is false conversely, i.e., not all optimal reversals can map to oriented gray edges; take = (-1, -2, -3) and r(2, 2) as an example. Besides, a reversal r oge complements the gray edges overlapping with oge. In other words, after applying r oge , oriented gray edges overlapping with oge become unoriented and vice versa. The heuristic used to compute P(oge) and select the maximum results from which we want to leave as many unoriented gray edges as possible after performing a reversal. Then, the algorithm is summarized as follows:
Figure 5

The reversal specified by a pair of blue parentheses comes from an oriented gray edge ( π i , π j ), in which i and j are even.

Approximation Algorithm for WGRP(w r = 1, 1 ≤ w bi < 2) (AAWGRP(1,1))

Input: A signed permutation .

Output: A sorting series composed of reversals and block-interchanges for transforming into .

1: Transform into its unsigned mapping π and construct BP(π);

2: While π is not sorted

3:   Repeatedly apply block-interchanges if Theorem 1 holds;

4:   Compute P(oge) for each oriented gray edge oge;

5:   Select the maximum P(oge) and perform the corresponding reversal;

6: End while;

7: Mimic the sorting series of π to I to the transformation between and ;

Lemma 5 After O(ϕ(π)) steps, the algorithm AAWGRP(1,1) stops and returns a sorting series for converting to .

Proof: Let π be the unsigned mapping of . The block-interchanges used in Step 3 and reversals in Step 5 have Δc bi = 2 and Δc r = 1, respectively. In other words, ϕ(π) = n + 1 - c(π) is strictly decreased after each applied operation. Due to this fact, AAWGRP(1,1) terminates after performing at most ϕ(π) operations.   □

Now, let us examine the time complexity of AAWGRP(1,1). Step1 and Step7 are mentioned in AWGRP(1,2), and the two steps require O(n) and O(n log n) time, respectively. To find two unoriented overlapping gray edges, a linear cost to scan π is sufficient. Applying a block-interchange also spends linear time, indicating that the running time to execute Step3 once is O(n). The computation of P(oge) for an oriented gray edge oge can be done simply by visiting the vertices that lay on the interval of oge one by one, and then counting the number of oriented and unoriented gray edges overlapping with oge, which costs O(n) time at most. Furthermore, at most n computations for P(oge) implies that Step4 can be done within O(n2) time. In Step5, an O(n)-time cost is needed to select the maximum P(oge) and next perform a corresponding reversal. Therefore, to apply a reversal, the time complexity is O(n2). Finally, AAWGRP(1,1) terminates after constructing at most ϕ(π) operations, and consequently, it takes at most O(n3) time in the worst case.

Comparing AAWGRP(1,1) with AWGRP(1,2), the former is preferable to the latter when analyzing oriented components provided that 1 ≤ w bi < 2. AAWGRP(1,1) seems feasible for producing a sorting scenario with a smaller sum of weights, but its performance in worst cases is the same as that of AWGRP(1,2) for solving WGRP(1, 1 ≤ w bi < 2). This is a consequence of certain specific permutations in which their weight sums conducted by both AAWGRP(1,1) and AWGRP(1,2) are far from the corresponding lower bounds. For example, if π has k oriented components, each with a 2-cycle only, in its BP(π), then both AAWGRP(1,1) and AWGRP(1,2) output k reversals; however, the lower bound is just when w r = w bi = 1. Due to the existence of these challenging cases, the approximation ratio of AAWGRP(1,1) is identical to that of AWGRP(1,2) when they are used to analyze WGRP(1, 1 ≤ w bi < 2).

WGRP(w r = 1, 3 ≤ w bi )

WGRP(1, 3 ≤ w bi ) can be easily solved by considering the fact that an arbitrary block-interchange can be mimicked by three specific reversals. For example, performing the block-interchange bi(2, 4, 6, 7) on = (2, - 5, -3, -4, -6, 7, 1) is the same as doing three reversals of r(2, 5), r(3, 7) and r(2, 4) in turn on . In other words, as long as a rearrangement sequence consists of a block-interchange, it can be replaced by three corresponding reversals without increasing the weighted sum. As a result, an ASBR is sufficient to optimally solve WGRP(1, 3 ≤ w bi ), and its best running-time to date is O(n3/2) [6].

Results and Discussion

Simulation

Despite the appearance of difficult cases with AAWGRP(1,1), it works well in the general situation, even very close to the lower bounds when w bi is near 2. To assess its performance, we conducted several experiments with the sample data generated by applying αn operations on = (1, 2, ..., n), where n {20, 50, 100} and α {0.1, 0.2, ..., 0.9, 1}. The rearrangement operations of either reversals or block-interchanges were selected randomly with equal probability, and each operation was specified at random by selecting two (for reversals) or four (for block-interchanges) integers ranging from 1 to n. Moreover, we examined 10n test cases and kept track of the mean for each pair of α and n.

At the beginning, we considered WGRP(1, 1). Then for the simulated data, we computed the corresponding lower bounds as well as the average weight sums of sorting sequences created by AAWGRP(1,1). For comparison, the results of AWGRP(1,2) were also marked (Figure 6). The weight sums of four sources, created series, AWGRP(1,2), AAWGRP(1,1) and lower bounds, increased with the number of applied operations, but at different rates. Furthermore, in the first three diagrams of Figure 6, regardless of the size n or the number of applied operations on permutations, the two curves corresponding to AAWGRP(1,1) and the lower bound exhibited the same relative behavior, with only a small gap between them (about 80% of the gaps between the curves were within 2 in the experiment of Figure 6c). This result indicates that AAWGRP(1,1) consistently produces a closer estimate of the exact dist(π) for WGRP(1, 1).
Figure 6

The diagrams (a), (b) and (c) consist of four curves each whereas (d) has four sets of curves, corresponding to the values of simulations and theoretical estimations. Specifically in (d), the expression of "AAWGRP(1,1)-1:1.3" means that AAWGRP(1,1) was used to solve WGRP(1, 1.3), and "lower bound-1:1.3" means the lower bound for WGRP(1, 1.3).

Subsequently, in Figure 6d, we fixed n = 100 and adjusted w bi = 1.3, 1.5, and 1.8 individually to investigate WGRP(1, 1.3), WGRP(1, 1.5), and WGRP(1, 1.8), respectively. Note that although three problems were included, we only plotted a curve to represent AWGRP(1,2). In addition to simplifying the chart, there was hardly any difference among the reconstructed sequences of AWGRP(1,2) for the three problems. In other words, the vast majority of operations in the sorting sequences of AWGRP(1,2) were reversals, and hence, their weight sums for the three problems were virtually identical. This phenomenon is expected based on two facts: First, the probability that a component will be unoriented is the same as that of a hurdle, which is Θ(n-2) on a random permutation of size n[26]. Second, the strategy of AWGRP(1,2) to remove oriented components is to use an ASBR to generate reversals. As a result, the components of the generated permutations are generally oriented, and the sorting sequences of AWGRP(1,2) consist mostly of reversals.

Notwithstanding AWGRP(1,2) was shown to be a factor 2 approximation algorithm for WGRP(1, 1) by Theorem 4, it is indeed infeasible in our experiments. The performance of AWGRP(1,2) is gradually improved as w bi moves towards 2 (Figure 6d). In contrast, AAWGRP(1,1) improves dramatically when 1 ≤ w bi < 2. Figure 6d suggests that the performance of AAWGRP(1,1) is superior to that of AWGRP(1,2) in such cases. Even in our simulation of w bi = 1.8, two curves of AAWGRP(1,1) and the lower bound were almost the same (most of their differences were less than 1).

Contribution

A large body of work has been devoted to genome rearrangement problems to study the evolutionary changes in the macrostructure of individual chromosomes according to the parsimonious principle. Here, we investigated the Weighted Genome Rearrangement Problem by considering reversals and block-interchanges simultaneously with various weight assignments, i.e., WGRP(w r , w bi ). Our objective was to find a rearrangement series composed of reversals and block-interchanges for converting to , as well as the most parsimonious series, that is, the minimum weight sum. We began studying the algorithm WGRP(w r , w bi ) by setting w r = 1 and w bi = 2, and then developed AWGRP(1,2) to optimally solve it. The idea used in AWGRP(1,2) is similar to that of Lin et al. [21] but differs when coping with unoriented components. We also provided a rigorous proof to show the correctness of AWGRP(1,2).

Furthermore, we adjusted the weight of block-interchanges so that 2 < w bi < 3 to study WGRP(1, 2 < w bi < 3). Two algorithms ASBR and AWGRP(1,2) were employed as approximation algorithms, whose ratios were given by Theorems 2 and 3, respectively. The approximation ratio of ASBR is , and hence it decreases if w bi is close to 3; however, the ratio of AWGRP(1,2) , which decreases when w bi is near 2. Even if both factors are at most 1.5 for 2 < w bi < 3, their behaviors are completely opposite. Consequently, we obtained a better result by always selecting the best output of the two algorithms to acquire a smaller approximation ratio around 1.225.

Later, the weight of block-interchanges is again varied to fit WGRP(1, 1 ≤ w bi < 2). To address this problem, we first showed that AWGRP(1,2) is a -approximation algorithm. Nevertheless, the factor becomes larger as w bi moves towards 1. From our experimental results on WGRP (1, 1), most of the weighted sums of sorting sequences provided by AWGRP(1,2) were more aggravated than the weighted sums of created sequences. Therefore, we improved it with AAWGRP(1,1) by adding a new component for selecting operations. Our idea was to choose as many best block-interchanges as possible, and determine plausible candidates for the best reversals once no best block-interchanges were available. As a heuristic, AAWGRP(1,1) does not have a smaller approximation ratio than AWGRP(1,2).

Consequently, we conducted several experiments to evaluate its performance and illustrated the results in Figure 6. Our result indicated that, although the theoretical approximation ratio of AAWGRP(1,1) trends towards 2 if w bi is close to 1, its average performance is significantly improved. Table 1 further summarizes our current and previous results for solving WGRP(w r , w bi ).
Table 1

Summary of our current and previous results for solving WGRP(w r , w bi ).

w r

w bi

Results

1

1 ≤ w bi < 2

2/w bi -app. with O(n3) time

 

2

O(n3/2)-time algorithm

 

2 <w bi < 3

1.225-app. with O(n3/2) time

 

3 ≤ w bi

O(n3/2)-time algorithm [6]

Conclusion

In this work, we present several approaches to examine genome rearrangement problems by considering reversals and block-interchanges together under various weight assignments. Provided that the weight of reversals is no more than that of block-interchanges, our algorithm reports an acceptable solution with theoretical guarantees and experimental evidences. Our results are promising, and these approaches should be used as an initial step for considering the two operations simultaneously. Future research must focus on improving both the approximation ratios and running times of these algorithms.

Declarations

Acknowledgements

We would like to thank the anonymous referees for many constructive comments during the revision. Part of this work was supported by the National Science Council (NSC) under grant NSC97-2221-E-182-033-MY3 and NSC96-2628-E-110-010-MY3.

Authors’ Affiliations

(1)
Department of Computer Science and Engineering, National Sun Yat-sen University
(2)
Department of Computer Science and Information Engineering, Chang Gung University

References

  1. Hannenhalli S, Pevzner PA: Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals. J ACM 1999, 46: 1–27. 10.1145/300515.300516View ArticleGoogle Scholar
  2. Kaplan H, Shamir R, Tarjan RE: A Faster and simpler algorithm for sorting signed permutations by reversals. SIAM J Comput 1999, 29: 880–892. 10.1137/S0097539798334207View ArticleGoogle Scholar
  3. Bergeron A: A very elementary presentation of the Hannenhalli-Pevzner theory. Dis Math 2005, 146: 134–145. 10.1016/j.dam.2004.04.010View ArticleGoogle Scholar
  4. Bergeron A, Mixtacki J, Stoye J: Reversal distance without hurdles and fortresses. In Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching: 5–7 July 2004; Istanbul, Turkey. Volume 3109. Edited by: Sahinalp SC, Muthukrishnan S, Dogrusöz U. Lecture Notes in Computer Science, Springer-Verlag; 2004:388–399.View ArticleGoogle Scholar
  5. Tannier E, Bergeron A, Sagot MF: Advances on sorting by reversals. Dis Math 2007, 155: 881–888. 10.1016/j.dam.2005.02.033View ArticleGoogle Scholar
  6. Han Y: Improving the Efficiency of Sorting by Reversals. In Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology: June 26–29 2006; Las Vegas, Nevada, USA. Edited by: Arabnia HR, Valafar H. CSREA Press; 2006:406–409.Google Scholar
  7. Swenson KM, Rajan V, Lin Y, Moret BME: Sorting signed permutations by inversions in O ( n log n ) time. In Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology: 18–21 May 2009; Tucson, Arizona. Volume 5541. Edited by: Batzoglou S. Lecture Notes in Computer Science, Springer-Verlag; 2009:386–399.Google Scholar
  8. Bader DA, Moret BME, Yan M: A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J Comput Biol 2001, 8: 483–491. 10.1089/106652701753216503View ArticlePubMedGoogle Scholar
  9. Bafna V, Pevzner PA: Sorting by transpositions. SIAM J Dis Math 1998, 11: 221–240.Google Scholar
  10. Hartman T, Shamir R: A simpler and faster 1.5-approximation algorithm for sorting by transpositions. Inf Comput 2006, 204: 275–290. 10.1016/j.ic.2005.09.002View ArticleGoogle Scholar
  11. Elias I, Hartman T: A 1.375-approximation algorithm for sorting by transpositions. IEEE/ACM Trans Comput Biol and Bioinformatics 2006, 3: 369–379. 10.1109/TCBB.2006.44View ArticleGoogle Scholar
  12. Christie DA: Sorting by block-interchanges. Inform Process Lett 1996, 60: 165–169. 10.1016/S0020-0190(96)00155-XView ArticleGoogle Scholar
  13. Lin YC, Lu CL, Chang HY, Tang CY: An efficient algorithm for sorting by block-interchanges and its application to the evolution of Vibrio species. J Comput Biol 2005, 12: 102–112. 10.1089/cmb.2005.12.102View ArticlePubMedGoogle Scholar
  14. Feng J, Zhu D: Faster algorithms for sorting by transpositions and sorting by block-interchanges. ACM T Algorithm 2007, 3: 1–14.Google Scholar
  15. Lin GH, Xue G: Signed genome rearrangement by reversals and transpositions: models and approximations. Theoret Comput Sci 2001, 259: 513–531. 10.1016/S0304-3975(00)00038-4View ArticleGoogle Scholar
  16. Walter MEMT, Dias Z, Meidanis J: Reversal and transposition distance of linear chromosomes. In Proceedings of String Processing and Information Retrieval: 9–11 September 1998; Santa Cruz, Bolivia. Edited by: Bolivia SCS. IEEE Computer Society; 1998:96–102.Google Scholar
  17. Gu QP, Peng S, Sudborough H: A 2-approximation algorithms for genome rearrangements by reversals and transpositions. Theoret Comput Sci 1999, 210: 327–339. 10.1016/S0304-3975(98)00092-9View ArticleGoogle Scholar
  18. Eriksen N: (1+ ε )-approximation of sorting by reversals and transpositions. Theoret Comput Sci 2002, 289: 517–529. 10.1016/S0304-3975(01)00338-3View ArticleGoogle Scholar
  19. Bader M, Ohlebusch E: Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions. J Comput Biol 2007, 14: 615–636. 10.1089/cmb.2007.R006View ArticlePubMedGoogle Scholar
  20. Yancopoulos S, Attie O, Friedberg R: Efficient sorting of genomic permutations by translocation, inversion & block interchange. Bioinformatics 2005, 21: 3340–3346. 10.1093/bioinformatics/bti535View ArticlePubMedGoogle Scholar
  21. Lin YC, Lu CL, Liu YH, Tang CY: SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges. Nucleic Acids Res 2006, 34: W696-W699. 10.1093/nar/gkl169PubMed CentralView ArticlePubMedGoogle Scholar
  22. Mira C, Meidanis J: Sorting by Block-Interchanges and Signed Reversals. In 4th International Conference on Information Technology: 2–4 April 2007; Las Vegas, Nevada, USA. Edited by: Latifi S. IEEE Computer Society; 2007:670–676.Google Scholar
  23. Bader M: Sorting by reversals, block interchanges, tandem duplications, and deletions. BMC Bio 2009, 10: S9. 10.1186/1471-2105-10-S1-S9View ArticleGoogle Scholar
  24. Vazirani VV: Approximation algorithms. New York: Springer-Verlag; 2001.Google Scholar
  25. El-Mabrouk N, Sankoff D: On the Reconstruction of Ancient Doubled Circular Genomes Using Minimum Reversal. Genome Informatics 1999, 10: 83–93.PubMedGoogle Scholar
  26. Swenson KM, Lin Y, Rajan V, Moret BME: Hurdles hardly have to be heeded. In Proceedings of the 6th RECOMB Comparative Genomics Satellite Workshop: 13–15 October 2008; Paris, France. Volume 5267. Edited by: Nelson CE, Vialette S. Lecture Notes in Computer Science, Springer-Verlag; 2008:241–251.Google Scholar
  27. Gog S, Bader M: Fast Algorithms for Transforming Back and Forth between a Signed Permutation and Its Equivalent Simple Permutation. J Comput Biol 2008, 15: 1029–1041. 10.1089/cmb.2008.0040View ArticlePubMedGoogle Scholar

Copyright

© Lin et al; licensee BioMed Central Ltd. 2009

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.