ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis.

Détails

ID Serval
serval:BIB_591EBB35D254
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis.
Périodique
RNA
Auteur⸱e⸱s
Vasa S.M., Guex N., Wilkinson K.A., Weeks K.M., Giddings M.C.
ISSN
1469-9001 (Electronic)
ISSN-L
1355-8382
Statut éditorial
Publié
Date de publication
10/2008
Peer-reviewed
Oui
Volume
14
Numéro
10
Pages
1979-1990
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, N.I.H., Extramural
Publication Status: ppublish
Résumé
Analysis of the long-range architecture of RNA is a challenging experimental and computational problem. Local nucleotide flexibility, which directly reports underlying base pairing and tertiary interactions in an RNA, can be comprehensively assessed at single nucleotide resolution using high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (hSHAPE). hSHAPE resolves structure-sensitive chemical modification information by high-resolution capillary electrophoresis and typically yields quantitative nucleotide flexibility information for 300-650 nucleotides (nt) per experiment. The electropherograms generated in hSHAPE experiments provide a wealth of structural information; however, significant algorithmic analysis steps are required to generate quantitative and interpretable data. We have developed a set of software tools called ShapeFinder to make possible rapid analysis of raw sequencer data from hSHAPE, and most other classes of nucleic acid reactivity experiments. The algorithms in ShapeFinder (1) convert measured fluorescence intensity to quantitative cDNA fragment amounts, (2) correct for signal decay over read lengths extending to 600 nts or more, (3) align reactivity data to the known RNA sequence, and (4) quantify per nucleotide reactivities using whole-channel Gaussian integration. The algorithms and user interface tools implemented in ShapeFinder create new opportunities for tackling ambitious problems involving high-throughput analysis of structure-function relationships in large RNAs.
Mots-clé
Algorithms, Base Sequence, Computational Biology/methods, Electrophoresis, Capillary, Nucleic Acid Conformation, Nucleotides/chemistry, RNA/chemistry, RNA/isolation & purification, Sequence Analysis, RNA/methods, Software
Pubmed
Web of science
Open Access
Oui
Création de la notice
29/01/2021 15:30
Dernière modification de la notice
30/01/2021 6:26
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