Related papers: Multiple sequence alignment for short sequences
High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
Long-term memory is a cornerstone of human intelligence. Enabling AI to process lifetime-scale information remains a long-standing pursuit in the field. Due to the constraints of full-attention architectures, the effective context length of…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
CSA is a web server for the comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue…
There now exist compact indexes that can efficiently list all the occurrences of a pattern in a dataset consisting of thousands of genomes, or even all the occurrences of all the pattern's maximal exact matches (MEMs) with respect to the…
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
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…
Network alignment generalizes and unifies several approaches for forming a matching or alignment between the vertices of two graphs. We study a mathematical programming framework for network alignment problem and a sparse variation of it…
Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the…
The development of neuromorphic hardware and modeling of biological neural networks requires algorithms with local learning rules. Artificial neural networks using local learning rules to perform principal subspace analysis (PSA) and…
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…
A new perspective is introduced regarding the analysis of Multiple Sequence Alignments (MSA), representing aligned data defined over a finite alphabet of symbols. The framework is designed to produce a block decomposition of an MSA, where…
Biological network alignment (NA) aims to identify similar regions between molecular networks of different species. NA can be local or global. Just as the recent trend in the NA field, we also focus on global NA, which can be pairwise (PNA)…
Multiple sequence alignment is a key process in today's biology, and finding a relevant alignment of several sequences is much more challenging than just optimizing some improbable evaluation functions. Our approach for addressing multiple…
Network alignment (NA) aims to find a node mapping between molecular networks of different species that identifies topologically or functionally similar network regions. Analogous to genomic sequence alignment, NA can be used to transfer…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
From molecular imaging to wireless communications, the ability to align and reconstruct signals from multiple misaligned observations is crucial for system performance. We study the problem of multi-reference alignment (MRA), which arises…
We introduce a method for manifold alignment of different modalities (or domains) of remote sensing images. The problem is recurrent when a set of multitemporal, multisource, multisensor and multiangular images is available. In these…