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Instability in progressive multiple sequence alignment algorithms
2015
Algorithms for Molecular Biology
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Conclusions: This has major ramifications for both the designers of large-scale multiple sequence alignment algorithms, and for the users of these alignments. ...
Results: We examine this tradeoff and find that, because of a loss of information in the early steps of the approach, the alignments generated by the most common multiple sequence alignment programs are ...
The power of progressive multiple sequence alignement may come from the fact that "more similar" sequences are aligned first: "...assuming that in progressive alignment, the best accuracy is obtained at ...
doi:10.1186/s13015-015-0057-1
pmid:26457114
pmcid:PMC4599319
fatcat:7cb2ibg2qjegvglynr6bh6xvlu
This Week in PNAS
2005
Proceedings of the National Academy of Sciences of the United States of America
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different in progressive multiple alignment. ...
''An algorithm for progressive multiple alignment of sequences with insertions'' by Ari Löytynoja and Nick Goldman (see pages 10557-10562)
MEDICAL SCIENCES
Epigenetic differences in identical twins ...
doi:10.1073/iti3005102
fatcat:pqmif5u43fhzdd2rerzqgmxrxq
Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family
2008
Algorithms for Molecular Biology
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Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments. ...
In case instabilities are observed, the sequences under consideration should be carefully checked for putative causes. ...
at Bielefeld University, and by the MPI for Mathematics in the Sciences in Leipzig. ...
doi:10.1186/1748-7188-3-15
pmid:18990223
pmcid:PMC2637874
fatcat:hdgw5rztzrgjbdyvdq3g5ai3nu
Current Trends and Ongoing Progress in the Computational Alignment of Biological Sequences
2019
IEEE Access
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INDEX TERMS Dynamic programming optimization, multiple sequence alignment, evolutionary computations, categories of sequence alignment, recent trends in sequence alignment, local and global alignment, ...
Researchers recently explore proposing novel computational techniques for simultaneous matching of multiple sequences or multiple sequence alignment (MSA). ...
Interrelations of sub-problems also mean that all pairwise alignments are linked through a tree in the process of progressive multiple sequence alignment. ...
doi:10.1109/access.2019.2916154
fatcat:yovnluecmbashh4bmqsi6cas4i
A Deterministic Analysis of Genome Integrity during Neoplastic Growth in Drosophila
2014
PLoS ONE
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While genome sequencing-based analysis of tumor genomes becomes increasingly a standard procedure in human cancer research, the potential necessity of genome instability for tumorigenesis in Drosophila ...
In various cancer types this process is enabled and accelerated by genome instability. ...
The increase of l s leads to an increase of the fraction of uniquely alignable sequences accompanied by a drop in the fraction of multiple alignments. ...
doi:10.1371/journal.pone.0087090
pmid:24516544
pmcid:PMC3916295
fatcat:vcl33z2ufzcdpnbl6d6oil7c7q
BioJava: an open-source framework for bioinformatics in 2012
2012
Bioinformatics
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Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. ...
ACKNOWLEDGEMENTS The authors thank everybody who contributed code, documentation or ideas, in particular A. Al-Hossary, R. Thornton, J. Warren, A. Draeger, G. Waldon and G. Barton. ...
Alignment module The alignment module supplies standard algorithms for sequence alignment and establishes a foundation to perform progressive multiple sequence alignments. ...
doi:10.1093/bioinformatics/bts494
pmid:22877863
pmcid:PMC3467744
fatcat:nx33nwr7f5aorcm7qbeogovfbq
Page 3483 of Mathematical Reviews Vol. , Issue 2004d
[page]
2004
Mathematical Reviews
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Progressive genomic instability and an arbitrary number of mutational stages are in- corporated. ...
Summary: “The problem of multiple sequence alignment is re- cast as an optimization problem using Markov decision theory. ...
Chapter 6: Structural Variation and Medical Genomics
2012
PLoS Computational Biology
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this recent attention is the result of the availability of higherresolution technologies for measuring these variants, including both microarray-based techniques, and more recently, high-throughput DNA sequencing ...
The latter class, called structural variants (SVs), have received considerable attention in the past several years as they are a previously under appreciated source of variation in human genomes. ...
On the other hand, if one allows reads whose alignment is ambiguous, then the problem of SV prediction requires an algorithm to distinguish among the multiple possible alignments for each read. ...
doi:10.1371/journal.pcbi.1002821
pmid:23300412
pmcid:PMC3531322
fatcat:bocxyjea4ranbgbek7qqy3olvy
Using deep reinforcement learning approach for solving the multiple sequence alignment problem
2019
SN Applied Sciences
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In this study, our proposed approach models the Multiple Sequence Alignment problem as a DRL problem and utilizes long short-term memory networks for estimation phase in the reinforcement learning algorithm ...
Multiple Sequence Alignment is the first step in solving many bioinformatics problems such as constructing phylogenetic trees. ...
Introduction Multiple Sequence Alignment (MSA) problem [1] is one of the most important problems in bioinformatics. ...
doi:10.1007/s42452-019-0611-4
fatcat:x2xxdesyubb5ne6nljh3a4lp7m
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
2015
Nucleic Acids Research
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in the pairwise alignments, used as building blocks in progressive alignment algorithms. ...
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. ...
ACKNOWLEDGEMENTS We thank Eli Levy Karin, Osnat Penn and Eyal Privman for insightful comments and Millie Montenegro for her help with comparing different alignment reliability algorithms. ...
doi:10.1093/nar/gkv318
pmid:25883146
pmcid:PMC4489236
fatcat:scwsthj4xjfvnm6yezd2q5s45i
Whole Exome Sequencing Data Analysis Algorithms in Cancer Diagnostics
[chapter]
2020
Prime Archives in Cancer Research
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Whole exome sequencing (WES) enables the analysis of all protein coding sequences in the human genome. ...
Variant calling algorithms for SNVs range from standalone tools to machine learning-based combined pipelines. Tools for CNV detection compare the number of reads aligned to a dedicated segment. ...
In addition, multiple targeted panels have also been accepted as targeted sequencing show comparable results in the detection of TMB status as exome sequencing [122] . ...
doi:10.37247/pacr.1.2020.5
fatcat:fb3xwm2drbhqhinmehksj3dgai
Home Monitoring Musculo-skeletal Disorders with a Single 3D Sensor
2013
2013 IEEE Conference on Computer Vision and Pattern Recognition Workshops
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In this paper, we propose a Temporal Alignment Spatial Summarization (TASS) method to decouple the complex spatio-temporal information of multiple Skeletal Action Units (SAU). ...
The subject is asked to perform several clinically validated standardized tests (e.g. sit-to-stand, repeated several times) in front of a 3D sensor to generate a sequence of skeletons (i.e. locations of ...
Algorithm. The key for solving Eq 2 lies in the Tem- poral Aligning Matrix A = {a i,j } Lx×Ly where a i,j = F(x i )−F(y j ) 2 . And in our case a i,j = (ζ x i −ζ y j ) 2 . ...
doi:10.1109/cvprw.2013.83
dblp:conf/cvpr/WangMWB13
fatcat:c5wg2nng3nf2vhbiyye7b4sdfq
Computational Biophysical, Biochemical, and Evolutionary Signature of Human R-Spondin Family Proteins, the Member of Canonical Wnt/β-Catenin Signaling Pathway
2014
BioMed Research International
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We approached this issue by interpreting the biochemical and biophysical properties along with molecular evolution of (Rspo)s thorough computational algorithm methods. ...
Through phylogenomics study, we developed a phylogenetic tree of sixty proteins (n=60) with the orthologs and paralogs seed sequences. Protein-protein network was also illustrated. ...
The clustal-omega server was organized on the basis of "progressive algorithm" [52] and the scoring system of the pairwise alignment algorithm is possibly the powerful component of the progressive algorithm ...
doi:10.1155/2014/974316
pmid:25276837
pmcid:PMC4172882
fatcat:qbmzseneu5d45im5i4ozmbwhwq
Recognition and Analysis of Abnormal Gait in Active Walking Rehabilitation Training
2017
Innovative Computing Information and Control Express Letters, Part B: Applications
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Finally, verification algorithm of local stationary characteristic based on dynamic time warping is established to recognize the progressive instability. ...
The experimental results revealed that the proposed method can effectively predict the progressive instability and fall gait, which can improve safety and intelligence of omni-directional walking training ...
As shown in Figure 7 , the person has progressive instability gait. ...
doi:10.24507/icicelb.08.11.1505
fatcat:6sbig5ss6ffapjaknnihv47hcq
CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data
2010
Computer applications in the biosciences : CABIOS
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New high-throughput sequencing technologies promise comprehensive characterization of CNAs. ...
We tested the method using the COLO-829 melanoma cell line sequenced to 40-fold coverage. ...
ACKNOWLEDGEMENT We acknowledge the assistance of Dr Phil Stephens of The Wellcome Trust Sanger Institute, UK, in providing the raw COLO-829 Affymetix SNP 6.0 array data. ...
doi:10.1093/bioinformatics/btq587
pmid:20966003
fatcat:lhfcgxucrfb35cmogajhlpkl2q
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