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Sequence coverage (or depth) is the number of unique reads that include a given nucleotide in the reconstructed sequence. [1] [2] Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. [3] Physical coverage, the cumulative length of reads or read pairs expressed as a multiple of ...
By expressing models in terms of the instantaneous rates of change we can avoid estimating a large numbers of parameters for each branch on a phylogenetic tree (or each comparison if the analysis involves many pairwise sequence comparisons). The models described on this page describe the evolution of a single site within a set of sequences.
Mamba [a] is a deep learning architecture focused on sequence modeling. It was developed by researchers from Carnegie Mellon University and Princeton University to address some limitations of transformer models, especially in processing long sequences. It is based on the Structured State Space sequence (S4) model. [2] [3] [4]
The residual connection stabilizes the training and convergence of deep neural networks with hundreds of layers, and is a common motif in deep neural networks, such as transformer models (e.g., BERT, and GPT models such as ChatGPT), the AlphaGo Zero system, the AlphaStar system, and the AlphaFold system.
For many years, sequence modelling and generation was done by using plain recurrent neural networks (RNNs). A well-cited early example was the Elman network (1990). In theory, the information from one token can propagate arbitrarily far down the sequence, but in practice the vanishing-gradient problem leaves the model's state at the end of a long sentence without precise, extractable ...
[4] [43] The current state-of-the-art in secondary structure prediction uses a system called DeepCNF (deep convolutional neural fields) which relies on the machine learning model of artificial neural networks to achieve an accuracy of approximately 84% when tasked to classify the amino acids of a protein sequence into one of three structural ...
DNA sequencing theory is the broad body of work that attempts to lay analytical foundations for determining the order of specific nucleotides in a sequence of DNA, otherwise known as DNA sequencing. The practical aspects revolve around designing and optimizing sequencing projects (known as "strategic genomics"), predicting project performance ...
In 2006, Next-Generation sequencing was first coupled with MNase digestion to explore nucleosome positioning and DNA sequence preferences in C. elegans,. [1] This was the first example of MNase-seq in any organism.