A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure (Q21093646)

Dimensions Publication ID

Dimensions

1025430652

5S Ribosomal RNA Database

10 August 2022

language of work or name

English

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publication date

2 July 2002

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published in

BMC Bioinformatics

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volume

3

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issue

1

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page(s)

18

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cites work

1 reference

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19 March 2017

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19 March 2017

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19 March 2017

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A general method applicable to the search for similarities in the amino acid sequence of two proteins

19 March 2017

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Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

19 March 2017

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A computational screen for methylation guide snoRNAs in yeast

19 March 2017

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A dynamic programming algorithm for RNA structure prediction including pseudoknots

19 March 2017

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19 March 2017

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Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2'-O-ribose methylation of rRNAs

6 April 2017

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Recent improvements to the SMART domain-based sequence annotation resource

19 March 2017

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Hidden Markov models in computational biology. Applications to protein modeling

7 April 2017

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Computational genomics of noncoding RNA genes

7 April 2017

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Discovering common stem-loop motifs in unaligned RNA sequences

12 September 2017

1 reference

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RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

Searching for patterns in genomic data

12 September 2017

1 reference

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Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

Compilation of small ribosomal subunit RNA structures

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

Stochastic context-free grammars for tRNA modeling

12 September 2017

1 reference

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Optimal alignments in linear space

12 September 2017

1 reference

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Comparing multiple RNA secondary structures using tree comparisons

12 September 2017

1 reference

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Compilation of tRNA sequences and sequences of tRNA genes

12 September 2017

1 reference

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Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome

27 September 2017

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Inferring consensus structure from nucleic acid sequences.

30 May 2018

1 reference

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Identifying potential tRNA genes in genomic DNA sequences

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

Pairwise RNA structure comparison with stochastic context-free grammars.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

The language of RNA: a formal grammar that includes pseudoknots.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

A polyhedral approach to RNA sequence structure alignment.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

Finding the hairpin in the haystack: searching for RNA motifs

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

RNAlign program: alignment of RNA sequences using both primary and secondary structures

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

An RNA pattern matching program with enhanced performance and portability.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

Automatic identification of group I intron cores in genomic DNA sequences.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=119854

Small subunit ribosomal RNA modeling using stochastic context-free grammars

29 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12095421

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Database on the structure of large ribosomal subunit RNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/12095421

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-3-18

1 reference

DBLP publication ID

journals/bmcbi/Eddy02

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1025430652

0 references

1 reference

1 reference

PubMed publication ID

12095421

1 reference