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A benchmark of multiple sequence alignment programs upon structural RNAs
scientific article
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instance of
scholarly article
1 reference
stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
title
A benchmark of multiple sequence alignment programs upon structural RNAs
(English)
1 reference
stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
main subject
sequence alignment
1 reference
based on heuristic
inferred from title
author
Stefan Washietl
series ordinal
3
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Andreas Wilm
object named as
Andreas Wilm
series ordinal
2
0 references
Paul P. Gardner
object named as
Paul P Gardner
series ordinal
1
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author name string
Stefan Washietl
series ordinal
3
1 reference
stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
language of work or name
English
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publication date
28 April 2005
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stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
published in
Nucleic Acids Research
1 reference
stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
volume
33
1 reference
stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
page(s)
2433-2439
1 reference
stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
issue
8
1 reference
stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
cites work
Accelerated probabilistic inference of RNA structure evolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Fast and reliable prediction of noncoding RNAs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
A probabilistic model for the evolution of RNA structure
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
A comprehensive comparison of comparative RNA structure prediction approaches
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Benchmarking tools for the alignment of functional noncoding DNA
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
RSEARCH: finding homologs of single structured RNA sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Pfold: RNA secondary structure prediction using stochastic context-free grammars
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Rfam: an RNA family database
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Noncoding RNA gene detection using comparative sequence analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
A comprehensive comparison of multiple sequence alignment programs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Amino acid substitution matrices from protein blocks
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Profile hidden Markov models
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Identification of common molecular subsequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
A general method applicable to the search for similarities in the amino acid sequence of two proteins
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Alignment of RNA base pairing probability matrices
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Secondary structure prediction for aligned RNA sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
24 March 2017
Multiple sequence alignment using partial order graphs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
7 April 2017
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
7 April 2017
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
7 April 2017
Predicting a set of minimal free energy RNA secondary structures common to two sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
27 September 2017
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
27 September 2017
RNA-related tools on the Bielefeld Bioinformatics Server
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
27 September 2017
Evolutionary HMMs: a Bayesian approach to multiple alignment
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
27 September 2017
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
27 September 2017
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
27 September 2017
RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
30 May 2018
A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
30 May 2018
Inferring consensus structure from nucleic acid sequences.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
30 May 2018
Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
30 May 2018
Align-m--a new algorithm for multiple alignment of highly divergent sequences.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
29 November 2018
Prediction of locally stable RNA secondary structures for genome-wide surveys.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
29 November 2018
Quality assessment of multiple alignment programs.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
29 November 2018
Displaying the information contents of structural RNA alignments: the structure logos.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
29 November 2018
An analysis of large rRNA sequences folded by a thermodynamic method.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
29 November 2018
RNA multi-structure landscapes. A study based on temperature dependent partition functions.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1087786
retrieved
29 November 2018
A hidden Markov model for progressive multiple alignment
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/15860779
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1093/NAR/GKI541
1 reference
stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
PMCID
1087786
0 references
PubMed ID
15860779
1 reference
stated in
Europe PubMed Central
PubMed ID
15860779
retrieved
2 July 2017
ResearchGate publication ID
7877038
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