StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction.

StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction.

MOTIVATION: Comparative modeling of RNA is known to be important for making accurate secondary structure predictions. RNA structure prediction tools such as PPfold or RNAalifold use an aligned set of sequences in predictions. Obtaining a multiple alignment from a set of sequences is quite a challen...

Bibliográfalaš dieđut
Váldodahkkit:	Arunapuram, P, Edvardsson, I, Golden, M, Anderson, J, Novák, A, Sükösd, Z, Hein, J
Materiálatiipa:	Journal article
Giella:	English
Almmustuhtton:	2013

Geahča maid

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees.
Dahkki: Novák, A, et al.
Almmustuhtton: (2008)

Quantifying variances in comparative RNA secondary structure prediction.
Dahkki: Anderson, J, et al.
Almmustuhtton: (2013)

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

Recursions for statistical multiple alignment.
Dahkki: Hein, J, et al.
Almmustuhtton: (2003)

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

Reticular alignment: a progressive corner-cutting method for multiple sequence alignment.
Dahkki: Szabó, A, et al.
Almmustuhtton: (2010)

A simulation-based approach to statistical alignment
Dahkki: Levy Karin, E, et al.
Almmustuhtton: (2018)

An algorithm for statistical alignment of sequences related by a binary tree.
Dahkki: Hein, J
Almmustuhtton: (2001)

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

Statistical problems in transport and alignment
Dahkki: Weed, Jonathan Daniel.
Almmustuhtton: (2019)

Approximate statistics of gapped alignments.
Dahkki: Mott, R, et al.
Almmustuhtton: (1999)

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

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

Statistical alignment: computational properties, homology testing and goodness-of-fit.
Dahkki: Hein, J, et al.
Almmustuhtton: (2000)

Gaussian alignments in statistical translation models
Dahkki: Mohammad, Ali (Ali H.)
Almmustuhtton: (2007)

Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps
Dahkki: Ohlson, Tomas, et al.
Almmustuhtton: (2010)

PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments
Dahkki: Caffrey, Daniel R, et al.
Almmustuhtton: (2010)

Aligning humanitarian surveys with international statistical standards
Dahkki: Schmieding, F
Almmustuhtton: (2021)

Alignment and Alignment Transition of Bent Core Nematics
Dahkki: Hegde, Gurumurthy, et al.
Almmustuhtton: (2013)

Bayesian coestimation of phylogeny and sequence alignment
Dahkki: Lunter, G, et al.
Almmustuhtton: (2005)

Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs
Dahkki: Herman, J, et al.
Almmustuhtton: (2015)

Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.
Dahkki: Herman, J, et al.
Almmustuhtton: (2014)

SpecAlign--processing and alignment of mass spectra datasets.
Dahkki: Wong, J, et al.
Almmustuhtton: (2005)

Vision by alignment
Dahkki: Kraft, Adam Davis
Almmustuhtton: (2018)

Alignment-free sequence comparison (I): statistics and power.
Dahkki: Reinert, G, et al.
Almmustuhtton: (2009)

The role of secondary algorithmic tacit collusion in achieving market alignment
Dahkki: Ezrachi, A, et al.
Almmustuhtton: (2024)

Evolutionary analyses of base-pairing interactions in DNA and RNA secondary structures
Dahkki: Golden, M, et al.
Almmustuhtton: (2019)

MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments.
Dahkki: Collingridge, P, et al.
Almmustuhtton: (2012)

Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.
Dahkki: Satija, R, et al.
Almmustuhtton: (2010)

Distribution of Aligned Letter Pairs in Optimal Alignments of Random Sequences
Dahkki: Hauser, R, et al.
Almmustuhtton: (2012)

Visual statistics 2.0 /
Dahkki: 379374 Doane, David P., et al.
Almmustuhtton: (2001)

Transparent Value Alignment: Foundations for Human-Centered Explainable AI in Alignment
Dahkki: Sanneman, Lindsay
Almmustuhtton: (2023)

Learning Aligned Cross-Modal Representations from Weakly Aligned Data
Dahkki: Castrejon, Lluis, et al.
Almmustuhtton: (2017)

Spectral Alignment of Graphs
Dahkki: Feizi, Soheil, et al.
Almmustuhtton: (2021)

Interference alignment by motion
Dahkki: Adib, Fadel M., et al.
Almmustuhtton: (2014)

Transparent Value Alignment
Dahkki: Sanneman, Lindsay, et al.
Almmustuhtton: (2023)

Interference Alignment and Cancellation
Dahkki: Gollakota, Shyamnath, et al.
Almmustuhtton: (2012)

Alignment of DNA sequences
Dahkki: Yang, Wen Wei
Almmustuhtton: (2008)

Spectral Alignment of Networks
Dahkki: Feizi, Soheil, et al.
Almmustuhtton: (2015)

Shaft alignment handbook /
Dahkki: Piotrowski, John, 1952-
Almmustuhtton: (2007)