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A Neural Multi-sequence Alignment TeCHnique (NeuMATCH)
, 2018 The alignment of heterogeneous sequential data (video to text) is an important and challenging problem. Standard techniques for this task, including Dynamic Time Warping (DTW) and Conditional Random Fields (CRFs), suffer from inherent drawbacks.
Dogan, Pelin +3 more
core +1 more source
FAMSA: Fast and accurate multiple sequence alignment of huge protein families [PDF]
Scientific Reports, 2016 Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment ...
Sebastian Deorowicz +2 more
semanticscholar +1 more source
Sequence alignment by passing messages [PDF]
BMC Genomics, 2014 Sequence alignment has become an indispensable tool in modern molecular biology research, and probabilistic sequence alignment models have been shown to provide an effective framework for building accurate sequence alignment tools. One such example is the pair hidden Markov model (pair-HMM), which has been especially popular in comparative sequence ...
openaire +3 more sources
Social context prevents heat hormetic effects against mutagens during fish development
FEBS Letters, EarlyView.This study shows that sublethal heat stress protects fish embryos against ultraviolet radiation, a concept known as ‘hormesis’. However, chemical stress transmission between fish embryos negates this protective effect. By providing evidence for the mechanistic molecular basis of heat stress hormesis and interindividual stress communication, this study ...
Lauric Feugere +5 more
wiley +1 more source
Fine-tuning structural RNA alignments in the twilight zone
BMC Bioinformatics, 2010 Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance.
Schirmer Stefanie +2 more
doaj +1 more source
Score distributions of gapped multiple sequence alignments down to the low-probability tail [PDF]
Phys. Rev. E 94, 022127 (2016), 2015 Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small.
arxiv +1 more source
Higher accuracy protein Multiple Sequence Alignment by Stochastic Algorithm [PDF]
, 2010 Multiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed.
Alpana Dey +4 more
core +1 more source
A Mutual Information Based Sequence Distance For Vertebrate Phylogeny Using Complete Mitochondrial Genomes [PDF]
, 2007 Traditional sequence distances require alignment. A new mutual information based sequence distance without alignment is defined in this paper. This distance is based on compositional vectors of DNA sequences or protein sequences from complete genomes ...
Anh, Vo +3 more
core +2 more sources
FEBS Letters, EarlyView.Spot‐14 and Spot‐14R play distinct roles in regulating metabolism in brown and beige adipocytes. While both influence lipid and glucose pathways, Spot‐14 uniquely controls thermogenic gene expression. This dual regulation balances energy storage and heat production, highlighting potential therapeutic targets for obesity and metabolic disorders. Spot 14
Lidia Itzel Castro‐Rodríguez +3 more
wiley +1 more source
BMC Bioinformatics, 2010 Background Large nucleotide sequence datasets are becoming increasingly common objects of comparison. Complete bacterial genomes are reported almost everyday. This creates challenges for developing new multiple sequence alignment methods.
Kryukov Kirill, Saitou Naruya
doaj +1 more source