Paper Info
Title
Oritfinder: A Web-Based Tool For The Identification Of Origin Of Transfers In Dna Sequences Of Bacterial Mobile Genetic Elements
Abstract
oriTfinder is a web server that facilitates the rapid identification of the origin of transfer site (oriT) of a conjugative plasmid or chromosome-borne integrative and conjugative element. The utilized backend database oriTDB was built upon more than one thousand known oriT regions of bacterial mobile genetic elements (MGEs) as well as the known MGE-encoding relaxases and type IV coupling proteins (T4CP). With a combination of similarity searches for the oriTDB-archived oriT nucleotide sequences and the co-localization of the flanking relaxase homologous genes, the oriTfinder can predict the oriT region with high accuracy in the DNA sequence of a bacterial plasmid or chromosome in minutes. The server also detects the other transfer-related modules, including the potential relaxase gene, T4CP gene and the type IV secretion system gene cluster, and the putative genes coding for virulence factors and acquired antibiotic resistance determinants. oriTfinder may contribute to meeting the increasing demands of re-annotations for bacterial conjugative, mobilizable or non-transferable elements and aid in the rapid risk accession of disease-relevant trait dissemination in pathogenic bacteria of interest. oriTfinder is freely available to all users without any login requirement at http://bioinfo-mml.sjtu.edu.cn/oriTfinder.
Year
DOI
Venue
2018
10.1093/nar/gky352
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
Chromosome,Biology,DNA,Mobile genetic elements,DNA sequencing,Computational biology,Web application,Genetics,Bodily secretions
Journal
46
Issue
ISSN
Citations 
W1
0305-1048
1
PageRank 
References 
Authors
0.37
7
7
Name
Order
Citations
PageRank
Xiaobin Li197.97
Yingzhou Xie231.10
Meng Liu33918.70
Cui Tai4304.19
Jingyong Sun510.71
Zixin Deng6395.74
Hong-Yu Ou7395.69