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Instability in progressive multiple sequence alignment algorithms

Kieran Boyce, Fabian Sievers, Desmond G. Higgins
2015 Algorithms for Molecular Biology  
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  
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

Holger Wagner, Burkhard Morgenstern, Andreas Dress
2008 Algorithms for Molecular Biology  
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

Muhammad Ishaq, Asfandyar Khan, Majid Khan, Muhammad Imran
2019 IEEE Access  
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

Cem Sievers, Federico Comoglio, Makiko Seimiya, Gunter Merdes, Renato Paro, Axel Imhof
2014 PLoS ONE  
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

A. Prlic, A. Yates, S. E. Bliven, P. W. Rose, J. Jacobsen, P. V. Troshin, M. Chapman, J. Gao, C. H. Koh, S. Foisy, R. Holland, G. Rimsa (+4 others)
2012 Bioinformatics  
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  
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

Benjamin J. Raphael, Fran Lewitter, Maricel Kann
2012 PLoS Computational Biology  
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

Reza Jafari, Mohammad Masoud Javidi, Marjan Kuchaki Rafsanjani
2019 SN Applied Sciences  
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

Itamar Sela, Haim Ashkenazy, Kazutaka Katoh, Tal Pupko
2015 Nucleic Acids Research  
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]

Áron Bartha, Balázs Gyorffy
2020 Prime Archives in Cancer Research  
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

Ruizhe Wang, Gerard Medioni, Carolee J. Winstein, Cesar Blanco
2013 2013 IEEE Conference on Computer Vision and Pattern Recognition Workshops  
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

Ashish Ranjan Sharma, Chiranjib Chakraborty, Sang-Soo Lee, Garima Sharma, Jeong Kyo Yoon, C. George Priya Doss, Dong-Keun Song, Ju-Suk Nam
2014 BioMed Research International  
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

Donghui Zhao, Junyou Yang, Yina Wang, Shuoyu Wang
2017 Innovative Computing Information and Control Express Letters, Part B: Applications  
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

Sergii Ivakhno, Tom Royce, Anthony J. Cox, Dirk J. Evers, R. Keira Cheetham, Simon Tavaré
2010 Computer applications in the biosciences : CABIOS  
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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