About: Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data

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About: Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data Goto Sponge NotDistinct Permalink

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

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data
Creator	Routh, Andrew Johnson, John
Source	Medline; PMC
abstract	We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa dynamically generates moving read segments. ViReMa initially attempts to align the 5′ end of a read to the reference genome(s) with the Bowtie seed-based alignment. A new read segment is then made by either extracting any unaligned nucleotides at the 3′ end of the read or by trimming the first nucleotide from the read. This continues iteratively until all portions of the read are either mapped or trimmed. With multiple reference genomes, it is possible to detect virus-to-host or inter-virus recombination. ViReMa is also capable of detecting insertion and substitution events and multiple recombination junctions within a single read. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome.
has issue date	2013-10-09(xsd:dateTime)
bibo:doi	10.1093/nar/gkt916
bibo:pmid	24137010
has license	cc-by
sha1sum (hex)	e141a069b6f6aef31ddf1a2ae592933db0b4a031
schema:url	https://doi.org/10.1093/nar/gkt916
resource representing a document's title	Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data
has PubMed Central identifier	PMC3902915
has PubMed identifier	24137010
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:e141a069b6f6aef31ddf1a2ae592933db0b4a031#body_text
is schema:about of	named entity 'sensitive' named entity 'multiple' named entity 'iteratively' named entity 'VIRUSES' named entity 'MAPPER' named entity 'POSSIBLE' named entity 'RATHER' named entity 'USED' named entity 'MOVING' named entity 'MAPPED' named entity 'SEED' named entity 'DETECTION' named entity 'MOTIFS' named entity 'TO PROVIDE' named entity 'HOST' named entity 'MAPPER' named entity 'GENOME' named entity 'MAPPING' named entity 'END' named entity 'DISTRIBUTION' named entity 'SEGMENTS' named entity 'ALGORITHM' named entity 'CONSERVED' named entity 'POSITIONS' named entity 'GENOMES' named entity 'REFERENCE' named entity 'VIRAL' named entity 'READ' named entity 'FLOCK HOUSE VIRUS' named entity 'EVENTS' named entity 'SEGMENT' named entity 'REGIONS' named entity 'TRIMMING' named entity '28S' named entity 'DETECTING' named entity 'USING' named entity 'NAMED' named entity 'LOCATED IN' named entity 'SUBSTITUTION' named entity 'RECOMBINATION' named entity 'CAPABLE' named entity 'PLATFORM' named entity 'BOWTIE' named entity 'INSERTION' named entity 'BASED' named entity 'DE NOVO' named entity 'DISCOVER' named entity 'NEXT-GENERATION SEQUENCING' named entity 'ANALYSIS' named entity 'SEQUENCING DATA' named entity 'FUNCTIONAL GENOMIC' named entity 'NEXT-GENERATION SEQUENCING' named entity 'MOTIFS' named entity 'RECOMBINATION' named entity 'VIRUS' named entity 'INTER-' named entity 'SEQUENCING DATA' named entity 'VIRUS' named entity 'REFERENCE GENOME' named entity 'INITIALLY' named entity 'MULTIPLE' named entity 'SINGLE' named entity 'EITHER' named entity 'EXTRACTING' named entity 'DISCOVERY' named entity 'VIRAL GENOME' named entity 'INFORMATION' named entity 'NEW' named entity 'SENSITIVE' named entity 'LENGTHS' named entity 'ALIGNMENT' named entity 'NUCLEOTIDE' named entity 'FUNCTIONAL' named entity 'NUCLEOTIDES' named entity 'TO DETECT' named entity 'RAPID' named entity 'ALIGN' named entity 'With' named entity 'insertion' named entity 'initially'

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