MODOMICS: a database of RNA modification pathways. 2017 update

Autoren

Pietro Boccaletto
Magdalena A Machnicka
Elzbieta Purta
Paweł Piątkowski
Błażej Bagiński
Tomasz K Wirecki
Valérie de Crécy-Lagard
Robert Ross
Patrick A Limbach
Annika Kotter
Mark Helm
Janusz M Bujnicki

DOI

10.1093/nar/gkx1030

eISSN

1362-4962

ISSN

0305-1048

Ausgabe der Veröffentlichung

D1

Zeitschrift

Nucleic Acids Research

Sprache

en

Online publication date

2017

Paginierung

D303 - D307

Datum der Veröffentlichung

2018

Status

Published

Herausgeber

Oxford University Press (OUP)

Herausgeber URL

http://dx.doi.org/10.1093/nar/gkx1030

Datum der Datenerfassung

2018

Titel

MODOMICS: a database of RNA modification pathways. 2017 update

Ausgabe der Zeitschrift

46

Datenquelle: Crossref

Abstract

MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. In the current database version, we included the following new features and data: extended mass spectrometry and liquid chromatography data for modified nucleosides; links between human tRNA sequences and MINTbase - a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments; new, machine-friendly system of unified abbreviations for modified nucleoside names; sets of modified tRNA sequences for two bacterial species, updated collection of mammalian tRNA modifications, 19 newly identified modified ribonucleosides and 66 functionally characterized proteins involved in RNA modification. Data from MODOMICS have been linked to the RNAcentral database of RNA sequences. MODOMICS is available at http://modomics.genesilico.pl.

Addresses

Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.

Autoren

Pietro Boccaletto
Magdalena A Machnicka
Elzbieta Purta
Pawel Piatkowski
Blazej Baginski
Tomasz K Wirecki
Valérie de Crécy-Lagard
Robert Ross
Patrick A Limbach
Annika Kotter
Mark Helm
Janusz M Bujnicki

DOI

10.1093/nar/gkx1030

eISSN

1362-4962

Externe Identifier

PubMed Identifier: 29106616
PubMed Central ID: PMC5753262

Funding acknowledgements

NIGMS NIH HHS: R01 GM058843
NIGMS NIH HHS: R01 GM070641

Open access

true

ISSN

0305-1048

Ausgabe der Veröffentlichung

D1

Zeitschrift

Nucleic acids research

Schlüsselwörter

Humans
RNA
RNA, Transfer
Ribonucleosides
Chromatography, Liquid
Databases, Genetic
Mass Spectrometry
Terminology as Topic

Sprache

eng

Medium

Print

Open access status

Open Access

Paginierung

D303 - D307

Datum der Veröffentlichung

2018

Status

Published

Publisher licence

CC BY-NC

Datum der Datenerfassung

2017

Titel

MODOMICS: a database of RNA modification pathways. 2017 update.

Sub types

Research Support, Non-U.S. Gov't
research-article
Journal Article

Ausgabe der Zeitschrift

46

Files

https://academic.oup.com/nar/article-pdf/46/D1/D303/23162078/gkx1030.pdf https://europepmc.org/articles/PMC5753262?pdf=render

Datenquelle: Europe PubMed Central

Abstract

MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. In the current database version, we included the following new features and data: extended mass spectrometry and liquid chromatography data for modified nucleosides; links between human tRNA sequences and MINTbase - a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments; new, machine-friendly system of unified abbreviations for modified nucleoside names; sets of modified tRNA sequences for two bacterial species, updated collection of mammalian tRNA modifications, 19 newly identified modified ribonucleosides and 66 functionally characterized proteins involved in RNA modification. Data from MODOMICS have been linked to the RNAcentral database of RNA sequences. MODOMICS is available at http://modomics.genesilico.pl.

Date of acceptance

2017

Autoren

Pietro Boccaletto
Magdalena A Machnicka
Elzbieta Purta
Pawel Piatkowski
Blazej Baginski
Tomasz K Wirecki
Valérie de Crécy-Lagard
Robert Ross
Patrick A Limbach
Annika Kotter
Mark Helm
Janusz M Bujnicki

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/29106616

DOI

10.1093/nar/gkx1030

eISSN

1362-4962

Externe Identifier

PubMed Central ID: PMC5753262

Funding acknowledgements

NIGMS NIH HHS: R01 GM058843
NIGMS NIH HHS: R01 GM070641

Ausgabe der Veröffentlichung

D1

Zeitschrift

Nucleic Acids Res

Schlüsselwörter

Chromatography, Liquid
Databases, Genetic
Humans
Mass Spectrometry
RNA
RNA, Transfer
Ribonucleosides
Terminology as Topic

Sprache

eng

Country

England

Paginierung

D303 - D307

PII

4584632

Datum der Veröffentlichung

2018

Status

Published

Datum, an dem der Datensatz öffentlich gemacht wurde

2019

Titel

MODOMICS: a database of RNA modification pathways. 2017 update.

Sub types

Journal Article
Research Support, Non-U.S. Gov't

Ausgabe der Zeitschrift

46

Datenquelle: PubMed

MODOMICS: a database of RNA modification pathways. 2017 update

Files

Werkzeuge