Results 61 to 70 of about 1,261,273 (206)
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction. [PDF]
, 2010 We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees.
Datta, Ruchira S +5 more
core +2 more sources
Parallel progressive multiple sequence alignment on reconfigurable meshes
BMC Genomics, 2011 Background One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance.
Nguyen Ken D, Pan Yi, Nong Ge
doaj +1 more source
An improved scoring matrix for multiple sequence alignment [PDF]
Mathematical Problems in Engineering, Vol. 2012, No. 490649, pp.
1-9, 2012, 2014 The way for performing multiple sequence alignment is based on the criterion of the maximum scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading to ambiguities in selecting the best alignment. This paper addresses this issue by introducing the concept of joint
arxiv +1 more source
Multiple sequence alignment by consensus [PDF]
Nucleic Acids Research, 1986 An algorithm for multiple sequence alignment is given that matches words of length and degree of mismatch chosen by the user. The alignment maximizes an alignment scoring function. The method is based on a novel extension of our consensus sequence methods.
openaire +3 more sources
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
BMC Bioinformatics, 2006 Background Existing tools for multiple-sequence alignment focus on aligning protein sequence or protein-coding DNA sequence, and are often based on extensions to Needleman-Wunsch-like pairwise alignment methods. We introduce a new tool, Sigma, with a new
Siddharthan Rahul
doaj +1 more source
Higher accuracy protein Multiple Sequence Alignment by Stochastic Algorithm [PDF]
, 2010 Multiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed.
Alpana Dey +4 more
core +1 more source
Limit cycles in piecewise-affine gene network models with multiple interaction loops [PDF]
, 2009 In this paper we consider piecewise affine differential equations modeling gene networks. We work with arbitrary decay rates, and under a local hypothesis expressed as an alignment condition of successive focal points. The interaction graph of the system
Farcot, Etienne, Gouzé, Jean-Luc
core +7 more sources
A statistical score for assessing the quality of multiple sequence alignments
BMC Bioinformatics, 2006 Background Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc.
Aittokallio Tero +3 more
doaj +1 more source
Fast sequence to graph alignment using the graph wavefront algorithm [PDF]
arXiv, 2022 Motivation: A pan-genome graph represents a collection of genomes and encodes sequence variations between them. It is a powerful data structure for studying multiple similar genomes. Sequence-to-graph alignment is an essential step for the construction and the analysis of pan-genome graphs. However, existing algorithms incur runtime proportional to the
arxiv
Segment-based multiple sequence alignment [PDF]
Bioinformatics, 2008 Abstract Motivation: Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use of alignment tools, progress in both categories is a contribution to the community and has driven research in the field so far. Results: We
Rausch, T. +5 more
openaire +4 more sources