Cargando…

Multiple sequence alignment accuracy and evolutionary distance estimation

BACKGROUND: Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation...

Descripción completa

Detalles Bibliográficos
Autor principal:	Rosenberg, Michael S
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2005
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1318491/ https://www.ncbi.nlm.nih.gov/pubmed/16305750 http://dx.doi.org/10.1186/1471-2105-6-278

Ejemplares similares

Evolutionary distance estimation and fidelity of pair wise sequence alignment
por: Rosenberg, Michael S
Publicado: (2005)

Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise
por: Dessimoz, Christophe, et al.
Publicado: (2008)

Grammar-based distance in progressive multiple sequence alignment
por: Russell, David J, et al.
Publicado: (2008)

The accuracy of several multiple sequence alignment programs for proteins
por: Nuin, Paulo AS, et al.
Publicado: (2006)

Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
por: Pervez, Muhammad Tariq, et al.
Publicado: (2014)

Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues
por: Lu, Yue, et al.
Publicado: (2009)

Comparison of phylogenetic trees through alignment of embedded evolutionary distances
por: Choi, Kwangbom, et al.
Publicado: (2009)

Estimating evolutionary distances between genomic sequences from spaced-word matches
por: Morgenstern, Burkhard, et al.
Publicado: (2015)

MAFFT version 5: improvement in accuracy of multiple sequence alignment
por: Katoh, Kazutaka, et al.
Publicado: (2005)

TM-Aligner: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy
por: Bhat, Basharat, et al.
Publicado: (2017)

MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences
por: Shen, Chengze, et al.
Publicado: (2021)

Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost
por: Yamada, Shinsuke, et al.
Publicado: (2006)

OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
por: Raghava, GPS, et al.
Publicado: (2003)

Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families
por: Hubley, Robert, et al.
Publicado: (2022)

A greedy alignment-free distance estimator for phylogenetic inference
por: Thankachan, Sharma V., et al.
Publicado: (2017)

Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
por: Sierk, Michael L, et al.
Publicado: (2010)

Parameterizing sequence alignment with an explicit evolutionary model
por: Rivas, Elena, et al.
Publicado: (2015)

Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model
por: Jayaraman, Gayathri, et al.
Publicado: (2010)

Distance metrics for ranked evolutionary trees
por: Kim, Jaehee, et al.
Publicado: (2020)

Estimates of statistical significance for comparison of individual positions in multiple sequence alignments
por: Sadreyev, Ruslan I, et al.
Publicado: (2004)

Auditory/visual distance estimation: accuracy and variability
por: Anderson, Paul W., et al.
Publicado: (2014)

Estimating true evolutionary distances under rearrangements, duplications, and losses
por: Lin, Yu, et al.
Publicado: (2010)

Estimation of the true evolutionary distance under the fragile breakage model
por: Alexeev, Nikita, et al.
Publicado: (2017)

Estimating true evolutionary distances under the DCJ model
por: Lin, Yu, et al.
Publicado: (2008)

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences
por: Dessimoz, Christophe, et al.
Publicado: (2006)

Next generation sequencing reads comparison with an alignment-free distance
por: Weitschek, Emanuel, et al.
Publicado: (2014)

Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty
por: Spielman, Stephanie J., et al.
Publicado: (2021)

Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques
por: Ortuño, Francisco M., et al.
Publicado: (2013)

Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina
por: Hallas, Joshua M., et al.
Publicado: (2017)

Multiple Sequence Alignment
Publicado: (2008)

Accuracy of structure-based sequence alignment of automatic methods
por: Kim, Changhoon, et al.
Publicado: (2007)

Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy
por: Aadland, Kelsey, et al.
Publicado: (2020)

Contextual Multiple Sequence Alignment
por: Gambin, Anna, et al.
Publicado: (2005)

Measuring the accuracy of genome-size multiple alignments
por: Prakash, Amol, et al.
Publicado: (2007)

MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments
por: Collingridge, Peter W, et al.
Publicado: (2012)

Alignment Modulates Ancestral Sequence Reconstruction Accuracy
por: Vialle, Ricardo Assunção, et al.
Publicado: (2018)

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences
por: Sahraeian, Sayed Mohammad Ebrahim, et al.
Publicado: (2010)

Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences
por: Bigot, Thomas, et al.
Publicado: (2019)

Curated multiple sequence alignment for the Adenomatous Polyposis Coli (APC) gene and accuracy of in silico pathogenicity predictions
por: Karabachev, Alexander D., et al.
Publicado: (2020)

POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments
por: Garrigan, Daniel
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_ildcl3itannllm6ms8r78vbedj