About: A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs
Creator	Armaos, Alexandros Marti, Stefanie Delli Ponti, Riccardo Dassi, Erik Gaetano Tartaglia, Gian Tartaglia, Gian Will, Sebastian
Source	Medline; PMC
abstract	To compare the secondary structure profiles of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure profile at single-nucleotide resolution and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. CROSSalign performs pair-wise comparisons and is able to find homologs between thousands of matches identifying the exact regions of similarity between profiles of different lengths. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modeling. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/crossalign.
has issue date	2018-12-03(xsd:dateTime)
bibo:doi	10.3389/fmolb.2018.00111
bibo:pmid	30560136
has license	cc-by
sha1sum (hex)	43b6759b989971eb0410fd45e7f97750183ed1bf
schema:url	https://doi.org/10.3389/fmolb.2018.00111
resource representing a document's title	A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs
has PubMed Central identifier	PMC6286970
has PubMed identifier	30560136
schema:publication	Front Mol Biosci
resource representing a document's body	covid:43b6759b989971eb0410fd45e7f97750183ed1bf#body_text
is schema:about of	named entity 'secondary structure' named entity 'recognizes' named entity 'resolution' named entity 'METHOD' named entity 'HTTP' named entity 'PROFILE' named entity 'COMBINATION' named entity 'AVAILABLE' named entity 'XIST' named entity 'HIV' named entity 'REPEAT' named entity 'SSRNA VIRUSES' named entity 'SEQUENCES' named entity 'COVARIANCE' named entity 'LONG NON-CODING RNAS' named entity 'METHODS' named entity 'DYNAMIC' named entity 'TIME' named entity 'DIFFERENT' named entity 'SUBMISSION' named entity 'FREELY' named entity 'LENGTHS' named entity 'ALGORITHM' named entity 'INCLUDING' named entity 'WISE' named entity 'SIMILARITY' named entity 'NUCLEOTIDE' named entity 'HOTAIR' named entity 'ALIGN' named entity 'APPLIED' named entity 'MATCHES' named entity 'REGIONS' named entity 'COMPUTATIONAL' named entity 'EXACT' covid:arg/43b6759b989971eb0410fd45e7f97750183ed1bf named entity 'RNA STRUCTURE PREDICTION' named entity 'WARPING' named entity 'POOL' named entity 'RNA' named entity 'STRUCTURE' named entity 'EVIDENCE FOR' named entity 'PREDICT' named entity 'DOMAIN' named entity 'MOLECULES' named entity 'SECONDARY STRUCTURE' named entity 'TO COMPARE' named entity 'BASED' named entity 'RECOGNITION' named entity 'CONSERVATION' named entity 'RNA SECONDARY STRUCTURE' named entity 'METHOD' named entity 'TO INVESTIGATE' named entity 'PAIR' named entity 'MODELING' named entity 'RESOLUTION' named entity 'IDENTIFYING' named entity 'STRUCTURAL' named entity 'COM' named entity 'WEBPAGE' named entity 'SINGLE' named entity 'Dynamic Time Warping (DTW)' named entity 'secondary structure' named entity 'sequences' named entity 'matches' named entity 'XIST' named entity 'homologs' named entity 'Dynamic Time Warping' named entity 'HIV' named entity 'non-coding RNAs' named entity 'Secondary Structure' named entity 'covariance' named entity 'lncRNAs' named entity 'Secondary Structure' named entity 'evolutionary conservation' named entity 'nucleotides'

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