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Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment
DIA is a mainstream method for quantitative proteomics, but consistent quantification across multiple LC-MS/MS instruments remains a bottleneck in...
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Fast Alignment
We’ve seen that optimal alignment is slow but accurate while exact matching is fast but cannot account for mutations. In this Chapter we tweak exact...
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Optimal Alignment
When we align two sequences, we in fact propose an evolutionary history for them. A history, where we account for three kinds of events, mutation,...
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Protein embedding based alignment
PurposeDespite the many progresses with alignment algorithms, aligning divergent protein sequences with less than 20–35% pairwise identity (so called...
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UniAligner: a parameter-free framework for fast sequence alignment
Even though the recent advances in ‘complete genomics’ revealed the previously inaccessible genomic regions, analysis of variations in centromeres...
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Sequence Alignment
New biological sequences do not emerge de novo in nature but rather are derived from pre-existing sequences. This foundational principle underlies...
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Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq
BackgroundParent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between...
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Pairwise Alignment, Multiple Alignment, and BLAST
Quantitative comparison of sequences can be performed pairwise by aligning two sequences based on considerations of gaps representing insertions or...
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EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment
BackgroundAdding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with...
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G-Aligner: a graph-based feature alignment method for untargeted LC–MS-based metabolomics
BackgroundLiquid chromatography–mass spectrometry is widely used in untargeted metabolomics for composition profiling. In multi-run analysis...
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Fast Alignment
We change into the directory for chapters, make the directory for this chapter, change into that, make the directory for this section, and change...
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Multiple Sequence Alignment
A multiple sequence alignment (MSA) is an alignment of three or more sequences. Given n strings S1, ... , Sn (...
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Optimal Alignment
We change into the chapter directory and make the directory for this chapter, 2. We change into that directory, make the directory for this section,...
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How Often Does Filtering of Alignment Columns Improve the Phylogenetic Inference of Two-Domain Proteins?
AbstractProtein phylogeny is usually reconstructed basing on a multiple alignment of amino acid sequences. One of the problems of such alignments is...
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Kinesin-7 CENP-E mediates chromosome alignment and spindle assembly checkpoint in meiosis I
In eukaryotes, meiosis is the genetic basis for sexual reproduction, which is important for chromosome stability and species evolution. The defects...
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Multilayer network alignment based on topological assessment via embeddings
BackgroundNetwork graphs allow modelling the real world objects in terms of interactions. In a multilayer network, the interactions are distributed...
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Phenol biodegradation using bio-filter tower packed column with immobilized bacterial consortium: a batch test study
The effluents from pulp and paper manufacturing industries contain high concentrations of phenol, which when discharged directly into surface water...
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LocARNA 2.0: Versatile Simultaneous Alignment and Folding of RNAs
Generating accurate alignments of non-coding RNA sequences is indispensable in the quest for understanding RNA function. Nevertheless, aligning RNAs...
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Alignment and integration of spatial transcriptomics data
Spatial transcriptomics (ST) measures mRNA expression across thousands of spots from a tissue slice while recording the two-dimensional (2D)...
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Scale-free dynamics in the core-periphery topography and task alignment decline from conscious to unconscious states
Scale-free physiological processes are ubiquitous in the human organism. Resting-state functional MRI studies observed the loss of scale-free...
