Multiple sequence alignment

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Related publications (31)

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

Jaume Bonet Martinez

Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...

OXFORD UNIV PRESS2021

Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols

In fishes, swimming performance is considered an important metric to measure fitness, dispersal and migratory abilities. The swimming performance of individual larval fishes is often integrated into models to make inferences on how environmental parameters ...

2021

Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures

David Atienza Alonso, Marina Zapater Sancho, Yasir Mahmood Qureshi, José Manuel Herruzo Ruiz

Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in next generation sequencing (NGS). As ...

2020

Statistical physics of interacting proteins: Impact of dataset size and quality assessed in synthetic sequences

Anne-Florence Raphaëlle Bitbol, Pierre Mergny

Identifying protein-protein interactions is crucial for a systems-level understanding of the cell. Recently, algorithms based on inverse statistical physics, e.g., direct coupling analysis (DCA), have allowed to use evolutionarily related sequences to addr ...

2020

MPGM: Scalable and Accurate Multiple Network Alignment

Matthias Grossglauser, Ehsan Kazemi

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

IEEE COMPUTER SOC2020

Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters

Ivan Istomin

Gene regulatory networks (GRNs) determine cellular behaviour, and ultimately the functioning of single- and multicellular organisms. Transcription factors regulate gene expression by binding to DNA or via remodelling chromatin. Recent advances in biotechno ...

EPFL2020

Ultraviolet Photodissociation of Peptides: New Insight on the Mobile Proton Model

Oleg Boyarkine, Aleksandr Pereverzev, Elizaveta Solovyeva

In this work, we study the mechanism of peptide photodissociation by ultraviolet irradiation at 193 nm wavelength and discuss the role of ionization proton in this process. We found that substituting the ionization proton for the alkali metal cations (sodi ...

PLEIADES PUBLISHING INC2020

Fast Transformers with Clustered Attention

François Fleuret, Angelos Katharopoulos, Apoorv Vyas

Transformers have been proven a successful model for a variety of tasks in sequence modeling. However, computing the attention matrix, which is their key component, has quadratic complexity with respect to the sequence length, thus making them prohibitivel ...

2020

An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma

Kalpani Anuradha Welivita

Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate s ...

ASSOC COMPUTING MACHINERY2019

Analysis of a Canonical Labeling Algorithm for the Alignment of Correlated Erdős-Rényi Graphs

Matthias Grossglauser, Negar Kiyavash, Osman Emre Dai

Graph alignment in two correlated random graphs refers to the task of identifying the correspondence between vertex sets of the graphs. Recent results have characterized the exact information-theoretic threshold for graph alignment in correlated Erdös-Rény ...

Association for Computing Machinery (ACM)2019

IMPACT: Interval-based Multi-pass Proteomic Alignment with Constant Traceback

James Richard Larus, Sahand Kashani, Stuart Anthony Byma

Darwin is a genomics co-processor that achieved a 15000x acceleration on long read assembly through innovative hardware and algorithm co-design. Darwins algorithms and hardware implementation were specifically designed for DNA analysis pipelines. This pape ...

2019

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