Related papers: Prefix reversals on binary and ternary strings
In this paper we study two operations, Pasting and Reversing, defined from a natural way to be applied over some rings such as the ring of polynomials and the ring of linear differential operators, which is a differential ring. We obtain…
One of the main challenges in Computational Biology is to find the evolutionary distance between two organisms. In the field of comparative genomics, one way to estimate such distance is to find a minimum cost sequence of rearrangements…
Using existing classification results for the 7- and 8-cycles in the pancake graph, we determine the number of permutations that require 4 pancake flips (prefix reversals) to be sorted. A similar characterization of the 8-cycles in the…
On the string of finite length, a (genomic) transposition is defined as the operation of exchanging two consecutive substrings. The minimum number of transpositions needed to transform one into the other is the transposition distance, that…
We study descriptive complexity properties of the class of regular bifix-free languages, which is the intersection of prefix-free and suffix-free regular languages. We show that there exist a single ternary universal (stream of) bifix-free…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
In this paper, we study the following problem: given $n$ subsets $S_1, \dots, S_n$ of an integer universe $U = \{0,\dots, u-1\}$, having total cardinality $N = \sum_{i=1}^n |S_i|$, find a prefix-free encoding $enc : U \rightarrow \{0,1\}^+$…
In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These…
In comparative genomics, a transposition is an operation that exchanges two consecutive sequences of genes in a genome. The transposition distance, that is, the minimum number of transpositions needed to transform a genome into another, is,…
Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
The number of zeros and the number of ones in a binary string are referred to as the composition of the string, and the prefix-suffix compositions of a string are a multiset formed by the compositions of the prefixes and suffixes of all…
The problem of answering rank/select queries over a bitmap is of utmost importance for many succinct data structures. When the bitmap does not change, many solutions exist in the theoretical and practical side. In this work we consider the…
Given a signed permutation on $n$ elements, we need to sort it with the fewest reversals. This is a fundamental algorithmic problem motivated by applications in comparative genomics, as it allows to accurately model rearrangements in small…
We study the following rearrangement problem: Given $n$ words, rearrange and concatenate them so that the obtained string is lexicographically smallest (or largest, respectively). We show that this problem reduces to sorting the given words…
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…
The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as the…
We consider a stack sorting algorithm where only the appropriate output values are popped from the stack and then any remaining entries in the stack are run through the stack in reverse order. We identify the basis for the $2$-reverse pass…
Prefix parsing asks whether an input prefix can be extended to a complete string generated by a given grammar. In the weighted setting, it also provides prefix probabilities, which are central to context-free language modeling,…
Previous compact representations of permutations have focused on adding a small index on top of the plain data $<\pi(1), \pi(2),...\pi(n)>$, in order to efficiently support the application of the inverse or the iterated permutation. In this…