Multiple sequence alignment

Summary

Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or

Official source

https://en.wikipedia.org/wiki/Multiple_sequence_alignment

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Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

Pierre Dumas

Oxford, Oxford University Press2006

Survival of rotational alignment in H-2 scattering from Si(100)

Christopher Scott Reilly

We report a state-prepared, state-resolved study of rotational scattering of a diatomic molecule from a solid surface. Specifically, H-2 molecules with 80 meV kinetic energy are rotationally aligned in the j = 3 rotational state via stimulated Raman pumping and then scattered from a Si(100) surface at normal incidence. The rotational alignment of the scattered molecules is determined by measuring, for both the incident and scattered molecules, the ionization yield of a probe laser, tuned to selectively ionize molecules in the j = 3 rotation level, as the probe laser polarization is rotated. The measurement is performed for two initial rotational alignments: a "helicoptering " alignment with the bonds constrained to lie primarily parallel to the surface and a "cartwheeling " alignment with the bonds lying primarily normal to the surface. For both initial alignments, the modulation of the probe ionization yield with laser polarization for the scattered molecules is pronounced, although significantly weaker than the modulation measured for the incident molecules. This indicates a significant modification but not a complete elimination of the initial alignment. The modulation is found to be stronger for the scattered molecules originating in the cartwheeling alignment than for the helicoptering alignment. These results contribute toward an improved understanding of the role of rotational motion in molecule-surface dynamics.

AIP Publishing2021

Network Alignment with Holistic Embeddings (Extended Abstract)

Quoc Viet Hung Nguyen, Thành Tâm Nguyên

Network alignment is the task of identifying topologically and semantically similar nodes across (two) different networks. However, existing alignment models either cannot handle large-scale graphs or fail to leverage different types of network information or modalities. In this paper, we propose a novel end-to-end alignment framework that can leverage different modalities to compare and align network nodes in an efficient way. A comprehensive evaluation on various datasets shows that our technique outperforms state-of-the-art approaches. Our source code is available at https://github.com/ thanhtrunghuynh93/holisticEmbeddingsNA.

IEEE COMPUTER SOC2022