Related papers: Multiple sequence alignment for short sequences

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…

In this paper we report on an algorithm for aligning multiple protein structures. The algorithm has been tested on a variety of inputs and it performs well in comparison to well-known algorithms for this problem.

Biological network alignment aims to identify similar regions between networks of different species. Existing methods compute node "similarities" to rapidly identify from possible alignments the "high-scoring" alignments with respect to the…

Most existing methods for unsupervised domain adaptation (UDA) rely on a shared network to extract domain-invariant features. However, when facing multiple source domains, optimizing such a network involves updating the parameters of the…

The Shortest Common Supersequence problem (SCS for short) consists in finding a shortest common supersequence of a finite set of words on a fixed alphabet Sigma. It is well-known that its decision version denoted [SR8] in [Garey and…

We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…

Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…

Mixed-integer optimisation problems can be computationally challenging. Here, we introduce and analyse two efficient algorithms with a specific sequential design that are aimed at dealing with sampled problems within this class. At each…

Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…

Cardiac magnetic resonance (CMR) image acquisition requires subjects to hold their breath while 2D cine images are acquired. This process assumes that the heart remains in the same position across all slices. However, differences in…

This paper investigates the approximability of the Longest Common Subsequence (LCS) problem. The fastest algorithm for solving the LCS problem exactly runs in essentially quadratic time in the length of the input, and it is known that under…

As in many other scientific domains, we face a fundamental problem when using machine learning to identify proteins from mass spectrometry data: large ground truth datasets mapping inputs to correct outputs are extremely difficult to…

Algorithms that detect covariance between pairs of columns in multiple sequence alignments are commonly employed to predict functionally important residues and structural contacts. However, the assumption that co-variance only occurs…

Recently, there has been great success in leveraging pre-trained large language models (LLMs) for time series analysis. The core idea lies in effectively aligning the modality between natural language and time series. However, the…

Permutation symmetries of deep networks make basic operations like model merging and similarity estimation challenging. In many cases, aligning the weights of the networks, i.e., finding optimal permutations between their weights, is…

Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the…

Many high-level procedural tasks can be decomposed into sequences of instructions that vary in their order and choice of tools. In the cooking domain, the web offers many partially-overlapping text and video recipes (i.e. procedures) that…

Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity…

Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…

In this paper, we consider a generalized longest common subsequence problem, in which a constraining sequence of length $s$ must be included as a substring and the other constraining sequence of length $t$ must be excluded as a subsequence…