Parameter advising for multiple sequence alignment [PDF]
BMC Bioinformatics, 2015 DeBlasio D, Kececioglu J.
europepmc +4 more sources
An entropy based heuristic model for predicting functional sub-type divisions of protein families [PDF]
, 2009 Multiple sequence alignments of protein families are often used for locating residues that are widely apart in the sequence, which are considered as influential for determining functional specificity of proteins towards various substrates, ligands, DNA ...
Bakis, Yasin +5 more
core +1 more source
Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment
BMC Bioinformatics, 2012 Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains.
Daniels Noah M +2 more
doaj +1 more source
A Linear Time Quantum Algorithm for Pairwise Sequence Alignment [PDF]
arXiv, 2023 Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been demonstrated which works by mapping the sequence alignment problem into a path-searching problem through a 2D graph.
arxiv
Process-oriented Iterative Multiple Alignment for Medical Process Mining
, 2017 Adapted from biological sequence alignment, trace alignment is a process mining technique used to visualize and analyze workflow data. Any analysis done with this method, however, is affected by the alignment quality.
Burd, Randall S. +4 more
core +1 more source
An Alternative Model of Amino Acid Replacement [PDF]
, 2004 The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution.
Altschul +27 more
core +3 more sources
Application of Sequence Embedding in Protein Sequence-Based Predictions [PDF]
arXiv, 2021 In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired by the development in natural language processing, several applications of sequence embedding have been observed.
arxiv
Sequence embedding for fast construction of guide trees for multiple sequence alignment
Algorithms for Molecular Biology, 2010 Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences.
Wilm Andreas +4 more
doaj +1 more source
The construction and use of log-odds substitution scores for multiple sequence alignment. [PDF]
PLoS Computational Biology, 2010 Most pairwise and multiple sequence alignment programs seek alignments with optimal scores. Central to defining such scores is selecting a set of substitution scores for aligned amino acids or nucleotides.
Stephen F Altschul +3 more
doaj +1 more source
Multiple alignment-free sequence comparison [PDF]
Bioinformatics, 2013 Abstract Motivation: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences.
Ren, J +4 more
openaire +4 more sources