Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.

Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.

MOTIVATION: Comparative genomic sequence analysis is a powerful approach for identifying putative functional elements in silico. The availability of full-genome sequences from many vertebrate species has resulted in the development of popular tools, for example, the phastCons software package that s...

Descrizione completa

Dettagli Bibliografici
Autori principali:	Satija, R, Hein, J, Lunter, G
Natura:	Journal article
Lingua:	English
Pubblicazione:	2010

Documenti analoghi

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.
di: Satija, R, et al.
Pubblicazione: (2008)

An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees.
di: Lunter, G, et al.
Pubblicazione: (2003)

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
di: Satija, R, et al.
Pubblicazione: (2009)

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
di: Miklós István, et al.
Pubblicazione: (2009-08-01)

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
di: Iyer Venky N, et al.
Pubblicazione: (2006-08-01)

Pairwise Versus Multiple Global Network Alignment
di: Vipin Vijayan, et al.
Pubblicazione: (2020-01-01)

Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.
di: Lunter, G
Pubblicazione: (2007)

Investigating selection on viruses: a statistical alignment approach.
di: de Groot, S, et al.
Pubblicazione: (2008)

Uncertainty in homology inferences: assessing and improving genomic sequence alignment.
di: Lunter, G, et al.
Pubblicazione: (2008)

Genome-wide identification of human functional DNA using a neutral indel model
di: Lunter, G, et al.
Pubblicazione: (2006)

Investigating selection on viruses: a statistical alignment approach
di: Lunter Gerton, et al.
Pubblicazione: (2008-07-01)

Recursions for statistical multiple alignment.
di: Hein, J, et al.
Pubblicazione: (2003)

Genome-wide identification of human functional DNA using a neutral indel model.
di: Gerton Lunter, et al.
Pubblicazione: (2006-01-01)

Designing multiple degenerate primers via consecutive pairwise alignments
di: Torabi Noorossadat, et al.
Pubblicazione: (2008-01-01)

Parallelized pairwise sequence alignment using CUDA on multiple GPUs
di: Jung Sungbo
Pubblicazione: (2009-06-01)

Gibbs sampler for statistical multiple alignment
di: Jensen, J, et al.
Pubblicazione: (2005)

A layout framework for genome-wide multiple sequence alignment graphs
di: Jeremias Schebera, et al.
Pubblicazione: (2024-08-01)

pmTM-align: scalable pairwise and multiple structure alignment with Apache Spark and OpenMP
di: Weiya Chen, et al.
Pubblicazione: (2020-09-01)

Genome-wide tracking of dCas9-methyltransferase footprints
di: Christina Galonska, et al.
Pubblicazione: (2018-02-01)

Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS
di: Kim Nora, et al.
Pubblicazione: (2012-07-01)

Genome-wide localization of mobile elements: experimental, statistical and biological considerations
di: Pan Wei, et al.
Pubblicazione: (2005-06-01)

RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.
di: Amir H Bayegan, et al.
Pubblicazione: (2020-01-01)

TSTA: thread and SIMD-based trapezoidal pairwise/multiple sequence-alignment method
di: Peiyu Zong, et al.
Pubblicazione: (2024-11-01)

Assessment on the performance of pairwise sequence alignment programs /
di: Muhammad Farhan Mohd. Tahir, 1994- , author
Pubblicazione: (2017)

Addressing sagittal plane imbalance in primary total knee arthroplasty: functional alignment outperforms kinematic and mechanical alignment techniques
di: Victor A. van de Graaf, et al.
Pubblicazione: (2024-08-01)

Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ
di: Ilia Minkin, et al.
Pubblicazione: (2020-06-01)

Following Ribosome Footprints to Understand Translation at a Genome Wide Level
di: Guillermo Eastman, et al.
Pubblicazione: (2018-01-01)

Visualizing profile-profile alignment: pairwise HMM logos.
di: Schuster-Böckler, B, et al.
Pubblicazione: (2005)

Fuzzy ant colony algorithm for pairwise sequence alignment /
di: Bahman Fakhr Sabahi, 1983-, et al.
Pubblicazione: (2012)

gpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences
di: Mostafa Hadian Dehkordi, et al.
Pubblicazione: (2011-06-01)

Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers
di: Grace, C, et al.
Pubblicazione: (2019)

Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers
di: Christopher Grace, et al.
Pubblicazione: (2019-11-01)

Human transposable elements in Repbase: genomic footprints from fish to humans
di: Kenji K. Kojima
Pubblicazione: (2018-01-01)

Improving pan-genome annotation using whole genome multiple alignment
di: Salzberg Steven L, et al.
Pubblicazione: (2011-06-01)

Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.)
di: Qing Lu, et al.
Pubblicazione: (2018-01-01)

Statistical physics of pairwise probability models
di: Yasser Roudi, et al.
Pubblicazione: (2009-11-01)

Universal internucleotide statistics in full genomes: a footprint of the DNA structure and packaging?
di: Mikhail I Bogachev, et al.
Pubblicazione: (2014-01-01)

Genome-wide comparative analysis of transposable elements in Palmae genomes
di: Mohanad A. Ibrahim, et al.
Pubblicazione: (2021-11-01)

The Use of Multiplicity Corrections, Order Statistics and Generalized Family-Wise Statistics with Application to Genome-Wide Studies.
di: Steven J Schrodi
Pubblicazione: (2016-01-01)

Flight quotas outperform focused mitigation strategies in reducing the carbon footprint of academic travel
di: Tamara Ben-Ari, et al.
Pubblicazione: (2024-01-01)