13Check_RNA: A tool to evaluate 13C chemical shift assignments of RNA

A. A. Icazatti; O. A. Martin; M. Villegas; I. Szleifer; J. A. Vila

doi:10.1093/bioinformatics/bty470

13Check_RNA: A tool to evaluate ¹³C chemical shift assignments of RNA

A. A. Icazatti^*, O. A. Martin, M. Villegas, I. Szleifer, J. A. Vila

^*Corresponding author for this work

Biomedical Engineering

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

Motivation: Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for evaluating the referencing of RNA ¹³C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Results: Based on an existent method we have implemented an open source python module to correct ¹³C CS (from here on ¹³C_exp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one.

Original language	English (US)
Pages (from-to)	4124-4126
Number of pages	3
Journal	Bioinformatics
Volume	34
Issue number	23
DOIs	https://doi.org/10.1093/bioinformatics/bty470
State	Published - Dec 1 2018

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bty470

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title = "13Check_RNA: A tool to evaluate 13C chemical shift assignments of RNA",

abstract = "Motivation: Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for evaluating the referencing of RNA 13C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Results: Based on an existent method we have implemented an open source python module to correct 13C CS (from here on 13Cexp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one.",

author = "Icazatti, {A. A.} and Martin, {O. A.} and M. Villegas and I. Szleifer and Vila, {J. A.}",

note = "Funding Information: This work was supported by Consejo Nacional de Investigaciones Cient{\'i}ficas y T{\'e}cnicas (PIP-0087) and Agencia Nacional de Promoci{\'o}n Cient{\'i}fica y Tecnol{\'o}gica (PICT-0767, PICT-0218), from Argentina. Publisher Copyright: {\textcopyright} The Author(s) 2018. Published by Oxford University Press. All rights reserved.",

year = "2018",

month = dec,

day = "1",

doi = "10.1093/bioinformatics/bty470",

language = "English (US)",

volume = "34",

pages = "4124--4126",

journal = "Bioinformatics",

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publisher = "Oxford University Press",

number = "23",

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TY - JOUR

T1 - 13Check_RNA

T2 - A tool to evaluate 13C chemical shift assignments of RNA

AU - Icazatti, A. A.

AU - Martin, O. A.

AU - Villegas, M.

AU - Szleifer, I.

AU - Vila, J. A.

N1 - Funding Information: This work was supported by Consejo Nacional de Investigaciones Científicas y Técnicas (PIP-0087) and Agencia Nacional de Promoción Científica y Tecnológica (PICT-0767, PICT-0218), from Argentina. Publisher Copyright: © The Author(s) 2018. Published by Oxford University Press. All rights reserved.

PY - 2018/12/1

Y1 - 2018/12/1

N2 - Motivation: Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for evaluating the referencing of RNA 13C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Results: Based on an existent method we have implemented an open source python module to correct 13C CS (from here on 13Cexp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one.

AB - Motivation: Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for evaluating the referencing of RNA 13C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Results: Based on an existent method we have implemented an open source python module to correct 13C CS (from here on 13Cexp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one.

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JO - Bioinformatics

JF - Bioinformatics

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ER -

13Check_RNA: A tool to evaluate ¹³C chemical shift assignments of RNA

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