Related papers: Faster exon assembly by sparse spliced alignment
Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…
We consider the problem of sorting $n$ elements in the case of \emph{persistent} comparison errors. In this model (Braverman and Mossel, SODA'08), each comparison between two elements can be wrong with some fixed (small) probability $p$,…
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
We propose a new algorithm for the fast solution of large, sparse, symmetric positive-definite linear systems, spaND -- sparsified Nested Dissection. It is based on nested dissection, sparsification and low-rank compression. After…
We initiate the study of approximation algorithms and computational barriers for constructing sparse $\alpha$-navigable graphs [IX23, DGM+24], a core primitive underlying recent advances in graph-based nearest neighbor search. Given an…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
In this paper, we implement Ant Colony Optimization (ACO) for sequence alignment. ACO is a meta-heuristic recently developed for nearest neighbor approximations in large, NP-hard search spaces. Here we use a genetic algorithm approach to…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
We study the problem of graph clustering where the goal is to partition a graph into clusters, i.e. disjoint subsets of vertices, such that each cluster is well connected internally while sparsely connected to the rest of the graph. In…
We design an algorithm for approximating the size of \emph{Max Cut} in dense graphs. Given a proximity parameter $\varepsilon \in (0,1)$, our algorithm approximates the size of \emph{Max Cut} of a graph $G$ with $n$ vertices, within an…
RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…
In this paper, we introduce a divide-and-conquer algorithm to improve sentence alignment speed. We utilize external bilingual sentence embeddings to find accurate hard delimiters for the parallel texts to be aligned. We use Monte Carlo…