IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico (Q27488811)

2

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Jun-Jie Hong

3

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Chung-Yung Chen

4

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Yuh-Show Tsai

Functional analyses of RNA structures shared between the internal ribosome entry sites of hepatitis C virus and the picornavirus porcine teschovirus 1 Talfan.

5

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publication date

27 May 2009

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published in

BMC Bioinformatics

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volume

10

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issue

1

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page(s)

160

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cites work

1 reference

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IRESite: the database of experimentally verified IRES structures (www.iresite.org).

20 March 2017

1 reference

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Rfam: annotating non-coding RNAs in complete genomes

20 March 2017

1 reference

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Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization

20 March 2017

1 reference

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Pfold: RNA secondary structure prediction using stochastic context-free grammars

20 March 2017

1 reference

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Rfam: an RNA family database

20 March 2017

1 reference

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Design of multistable RNA molecules

20 March 2017

1 reference

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Structure of the 30S ribosomal subunit

20 March 2017

1 reference

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Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution

20 March 2017

1 reference

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The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

20 March 2017

1 reference

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Alterations to both the primary and predicted secondary structure of stem-loop IIIc of the hepatitis C virus 1b 5' untranslated region (5'UTR) lead to mutants severely defective in translation which cannot be complemented in trans by the [...]

20 March 2017

1 reference

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Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA

20 March 2017

1 reference

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Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA

20 March 2017

1 reference

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Relevance of RNA structure for the activity of picornavirus IRES elements

20 March 2017

1 reference

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Divergent picornavirus IRES elements

20 March 2017

1 reference

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Identification of the hepatitis A virus internal ribosome entry site: in vivo and in vitro analysis of bicistronic RNAs containing the HAV 5' noncoding region

20 March 2017

1 reference

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Structural requirements for initiation of translation by internal ribosome entry within genome-length hepatitis C virus RNA

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Hepatitis C virus-related internal ribosome entry sites are found in multiple genera of the family Picornaviridae.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Functional and structural similarities between the internal ribosome entry sites of hepatitis C virus and porcine teschovirus, a picornavirus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

The accuracy of ribosomal RNA comparative structure models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

The use of bi-cistronic transfer vectors for the baculovirus expression system

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Translation initiation: adept at adapting

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Translation initiation factor eIF4B interacts with a picornavirus internal ribosome entry site in both 48S and 80S initiation complexes independently of initiator AUG location.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

UTRdb: a specialized database of 5' and 3' untranslated regions of eukaryotic mRNAs.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

UTRdb: a specialized database of 5'- and 3'-untranslated regions of eukaryotic mRNAs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Intact eukaryotic initiation factor 4G is required for hepatitis A virus internal initiation of translation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Complete nucleotide sequence of enterovirus 71 is distinct from poliovirus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Polioviruses containing picornavirus type 1 and/or type 2 internal ribosomal entry site elements: genetic hybrids and the expression of a foreign gene

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

In vitro translation of poliovirus RNA: utilization of internal initiation sites in reticulocyte lysate

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Cap-independent translation of picornavirus RNAs: structure and function of the internal ribosomal entry site

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Translation of poliovirus rna in vitro: Changes in cleavage pattern and initiation sites by ribosomal salt wash

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

The complete nucleotide sequence of a bovine enterovirus

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Prediction of locally stable RNA secondary structures for genome-wide surveys

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Enterovirus 71 contains a type I IRES element that functions when eukaryotic initiation factor eIF4G is cleaved.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

RnaViz 2: an improved representation of RNA secondary structure.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

A general edit distance between RNA structures.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Hepatitis C virus: an infectious molecular clone of a second major genotype (2a) and lack of viability of intertypic 1a and 2a chimeras

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Mutational analysis of two unstructured domains of the 5' untranslated region of HCV RNA.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2698906

Application of genome sequence information to the classification of bovine enteroviruses: the importance of 5'- and 3'-nontranslated regions

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19473520

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Thermodynamics of three-way multibranch loops in RNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19473520

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-10-160

1 reference

DBLP publication ID

journals/bmcbi/WuHHCT09

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1013266811

0 references

Fatcat ID

release_ppo6qkvsfffz5ksvl3oznlykgm

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ppo6qkvsfffz5ksvl3oznlykgm

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

1 reference

PubMed publication ID

19473520

1 reference