Propositionalisation of multiple sequence alignments using probabilistic models [PDF]
, 2008 Multiple sequence alignments play a central role in Bioinformatics. Most alignment representations are designed to facilitate knowledge extraction by human experts.
Holmes, Geoffrey +2 more
core +2 more sources
SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation
BMC Bioinformatics, 2011 Background Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields.
Strope Cory L +2 more
doaj +1 more source
Molecules, 2018 Residues in proteins that are in close spatial proximity are more prone to covariate as their interactions are likely to be preserved due to structural and evolutionary constraints.
Patrice Koehl +2 more
doaj +1 more source
Improving spliced alignment for identification of ortholog groups and multiple CDS alignment [PDF]
arXiv, 2017 The Spliced Alignment Problem (SAP) that consists in finding an optimal semi-global alignment of a spliced RNA sequence on an unspliced genomic sequence has been largely considered for the prediction and the annotation of gene structures in genomes.
arxiv
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee [PDF]
, 2017 Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database.
Armougom, Fabrice +7 more
core
Locality Sensitive Hashing-based Sequence Alignment Using Deep Bidirectional LSTM Models [PDF]
arXiv, 2020 Bidirectional Long Short-Term Memory (LSTM) is a special kind of Recurrent Neural Network (RNN) architecture which is designed to model sequences and their long-range dependencies more precisely than RNNs. This paper proposes to use deep bidirectional LSTM for sequence modeling as an approach to perform locality-sensitive hashing (LSH)-based sequence ...
arxiv
CSA: An efficient algorithm to improve circular DNA multiple alignment
BMC Bioinformatics, 2009 Background The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes.
Pereira Luísa +2 more
doaj +1 more source
CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment
BMC Bioinformatics, 2017 Background The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep its running time in an acceptable ...
Xi Chen +4 more
doaj +1 more source
An Optimized System for Multiple Sequence Alignment
2009 International Conference on Reconfigurable Computing and FPGAs, 2009 Multiple sequence alignment (MSA) is one of the essential operations for identifying functional and structural relations among proteins. The execution of an MSA algorithm requires high-performance platforms. This paper presents a hardware system that speeds up the popular MSA software ClustalW.
Yilmaz, Caglar, Gok, Mustafa
openaire +3 more sources
Integrated multiple sequence alignment [PDF]
, 2005 Sammeth M. Integrated multiple sequence alignment. Bielefeld (Germany): Bielefeld University; 2005.The thesis presents enhancements for automated and manual multiple sequence alignment: existing alignment algorithms are made more easily accessible and ...
Sammeth, Michael
core +1 more source