Multiple Sequence Alignment
18 papers with code • 3 benchmarks • 0 datasets
Benchmarks
These leaderboards are used to track progress in Multiple Sequence Alignment
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Latest papers with no code
Application of Sequence Embedding in Protein Sequence-Based Predictions
In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix.
A Simple Algorithm for the Constrained Sequence Problems
In this paper, we present a simple algorithm to solve the constrained longest common subsequence problem in $O(n \cdot m \cdot r)$ time and show that the constrained longest common subsequence problem is equivalent to a special case of the constrained multiple sequence alignment problem which can also be solved.
Pairwise heuristic sequence alignment algorithm based on deep reinforcement learning
Various methods have been developed to analyze the association between organisms and their genomic sequences.
Neural Time Warping For Multiple Sequence Alignment
Multiple sequences alignment (MSA) is a traditional and challenging task for time-series analyses.
Boltzmann machine learning and regularization methods for inferring evolutionary fields and couplings from a multiple sequence alignment
Both averages smoothly change and converge, but their learning profiles are very different between learning methods.
Seq-SetNet: Exploring Sequence Sets for Inferring Structures
Therefore, the traditional deep neural networks designed for image processing cannot be directly applied on sequence sets.
Privacy Preserving Location Data Publishing: A Machine Learning Approach
By introducing a new formulation of the problem, we are able to apply machine learning algorithms for clustering the trajectories and propose to use $k$-means algorithm for this purpose.
Influence of Multiple Sequence Alignment Depth on Potts Statistical Models of Protein Covariation
We show how as MSA depth $N$ decreases an "overfitting" effect occurs such that sequences in the training MSA have overestimated fitness, and we predict the magnitude of this effect and discuss how regularization can help correct for it, use a regularization procedure motivated by statistical analysis of the effects of finite sampling.
Multiple Sequence Alignment is not a Solved Problem
Several criteria have been developed by biologists to help them identify potential homologies (compositional, ontogenetic, topographical and functional similarity, plus conjunction and congruence), and these criteria can be applied to molecular data, in principle.
Full Reconstruction of Non-Stationary Strand-Symmetric Models on Rooted Phylogenies
We prove that the location of the root and the full model can be identified and statistically consistently estimated for a non-stationary, strand-symmetric substitution model given a multiple sequence alignment with two or more sequences.
