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Semiautomated improvement of RNA alignments
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scholarly article
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title
Semiautomated improvement of RNA alignments
(English)
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author
Jan Gorodkin
series ordinal
11
object named as
Jan Gorodkin
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author name string
Ebbe S Andersen
series ordinal
1
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Allan Lind-Thomsen
series ordinal
2
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Bjarne Knudsen
series ordinal
3
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Susie E Kristensen
series ordinal
4
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Jakob H Havgaard
series ordinal
5
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Elfar Torarinsson
series ordinal
6
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Niels Larsen
series ordinal
7
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Christian Zwieb
series ordinal
8
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Peter Sestoft
series ordinal
9
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Jørgen Kjems
series ordinal
10
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language of work or name
English
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publication date
November 2007
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published in
RNA
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volume
13
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issue
11
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page(s)
1850-9
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cites work
4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing
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7 April 2017
Accelerated probabilistic inference of RNA structure evolution
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7 April 2017
Rfam: annotating non-coding RNAs in complete genomes
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7 April 2017
A comprehensive comparison of comparative RNA structure prediction approaches
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7 April 2017
Pfold: RNA secondary structure prediction using stochastic context-free grammars
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7 April 2017
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7 April 2017
RNA sequence analysis using covariance models
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7 April 2017
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
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7 April 2017
The Jalview Java alignment editor
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7 April 2017
Vienna RNA secondary structure server
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7 April 2017
Comparative functional study of the viral telomerase RNA based on natural mutations
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7 April 2017
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
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7 April 2017
Alignment of RNA base pairing probability matrices
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7 April 2017
Secondary structure prediction for aligned RNA sequences
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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7 April 2017
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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7 April 2017
ARB: a software environment for sequence data
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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7 April 2017
Multiple structural alignment and clustering of RNA sequences
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
CMfinder--a covariance model based RNA motif finding algorithm
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
Predicting a set of minimal free energy RNA secondary structures common to two sequences
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
RALEE--RNA ALignment editor in Emacs
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
The non-Watson-Crick base pairs and their associated isostericity matrices
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
RNAML: a standard syntax for exchanging RNA information.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure
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28 September 2017
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
MView: a web-compatible database search or multiple alignment viewer
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
Finding the most significant common sequence and structure motifs in a set of RNA sequences
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
Stochastic context-free grammars for tRNA modeling
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28 September 2017
Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
Selection of representative protein data sets
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 September 2017
Evolutionary rate variation and RNA secondary structure prediction.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 November 2018
Pairwise RNA structure comparison with stochastic context-free grammars.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2040093
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28 November 2018
Semi-automated update and cleanup of structural RNA alignment databases.
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=2040093
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28 November 2018
DCSE, an interactive tool for sequence alignment and secondary structure research
1 reference
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12 December 2020
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inferred from PubMed ID database lookup
Identifiers
DOI
10.1261/RNA.215407
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PMCID
2040093
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PubMed ID
17804647
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ResearchGate publication ID
6035186
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