About: JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences
Creator	Upton, Chris Barsky, Marina Kruczkiewicz, Peter Marass, Francesco Sadeque, Aliya
source	Medline; PMC
abstract	We describe the use of Java Pattern Finder (JaPaFi) to identify short (<100 nt) highly conserved sequences in a series of poxvirus genomes. The algorithm utilizes pattern matching to identify approximate matches appearing at least once in each member of a set of genomes; a key feature is that the genomes do not need to be aligned. The user simply specifies the genomes to search, minimum length of sequences to find and the maximum number of mismatches and indels allowed. Many of the most highly conserved segments contain poxvirus promoter elements.
has issue date	2010-08-31(xsd:dateTime)
bibo:doi	10.3390/v2091867
bibo:pmid	21994712
has license	cc-by
sha1sum (hex)	673c840a9c907075a0591aee62cb8a7b15133a10
schema:url	https://doi.org/10.3390/v2091867
resource representing a document's title	JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences
has PubMed Central identifier	PMC3185747
has PubMed identifier	21994712
schema:publication	Viruses
resource representing a document's body	covid:673c840a9c907075a0591aee62cb8a7b15133a10#body_text
is schema:about of	named entity 'SERIES' named entity 'CONTAIN' named entity 'MATCHES' named entity 'ALIGNED' named entity 'USE OF' named entity 'poxvirus' named entity 'indels' named entity 'Highly Conserved' named entity 'genome' named entity 'MEME' named entity 'promoter element' named entity 'coding regions' named entity 'E-value' named entity 'protein sequences' named entity 'EMBOSS' named entity 'Yatapoxvirus' named entity 'poxviruses' named entity 'poxvirus' named entity 'bioinformatics' named entity 'database' named entity 'protein repertoire' named entity 'Longest Common Substring' named entity 'ribosomal' named entity 'database' named entity 'codons' named entity 'gene' named entity 'genome' named entity 'poxvirus' named entity 'nucleotide' named entity 'cytoplasm' named entity 'polypeptide' named entity 'Poxvirus' named entity 'Protein' named entity 'codon degeneracy' named entity 'genome map' named entity 'graphical interface' named entity 'e-value' named entity 'poxviruses' named entity 'non-coding' named entity 'DNA sequences' named entity 'genomes' named entity 'virus' named entity 'codons' named entity 'kDa' named entity 'GC content' named entity 'evolution' named entity 'viruses' named entity 'mRNA' named entity 'PROSITE' named entity 'superfamilies' named entity 'conserved sequence' named entity 'PROSITE' named entity 'Viral' named entity 'protein' named entity 'protein domain' named entity 'amino acids' named entity 'genome sequences' named entity 'consensus sequences' named entity 'DNA-dependent RNA polymerase' named entity 'genomes' named entity 'virus' named entity 'Kozak sequence' named entity 'database' named entity 'RNA pseudoknot' named entity 'nucleotides' named entity 'complement' named entity 'NCBI' named entity 'algorithm' named entity 'Yaba Monkey Tumor Virus' named entity 'DNA sequence' named entity 'control sequences' named entity 'database' named entity 'database' named entity 'Kozak sequence' named entity '60,000' named entity 'promoter elements' named entity 'methionine'

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