Reference - free detection of isolated SNPs Additional File 1
نویسندگان
چکیده
1University of Bordeaux, CNRS / LaBRI, F-33405 Talence, France, 2University of Bordeaux, CBiB, F-33000 Bordeaux, France, 3INRA, UMR1349 IGEPP, Le Rheu, France, 4GenScale, INRIA Rennes Bretagne-Atlantique, IRISA, Rennes, France, 5BAMBOO, INRIA Grenoble Rhone-Alpes, Lyon, France, 6Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1 UMR CNRS 5558, Lyon, France, 7INRA, UMR1300 Biology, Epidemiology and Risk Analysis in Animal Health, Nantes, France, 8LUNAM University, Oniris, Nantes Atlantic College of Veterinary Medicine and Food Sciences and Engineering, UMR BioEpAR, Nantes, France and 9Department of Computer Science and Engineering, The Pennsylvania State University, USA
منابع مشابه
Reference-free detection of isolated SNPs
Detecting single nucleotide polymorphisms (SNPs) between genomes is becoming a routine task with next-generation sequencing. Generally, SNP detection methods use a reference genome. As non-model organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have fundamental limitations: they can only call SNPs between...
متن کاملWhole genome sequencing of a single Bos taurus animal for SNP discovery
Background: The majority of the 2 million bovine SNPs currently available in dbSNP have been identified in a single breed, Hereford cattle, during the bovine genome project. In an attempt to evaluate the variance of a second breed, we have produced a whole genome sequence at low coverage of a single Fleckvieh bull. Results: We generated 24 gigabases of sequence, mainly using 36-bp paired-end re...
متن کاملSingle Nucleotide Polymorphisms and Association Studies: A Few Critical Points
Uncovering DNA sequence variations that correlate with phenotypic changes, e.g., diseases, is the aim of sequence variation studies. Common types sequence variations are Single nucleotide polymorphism (SNP, pronounced snip).SNPs are the third-generation molecular marker. SNP represents a DNA sequence variant of a single base pair with the minor allele occurring in more than 1% of a given popula...
متن کاملInvestigation of fimH Single Nucleotide Polymorphisms (C640T and T591A) in Uropathogenic E. coli Isolated from Patients with Urinary Tract Infections
Background: Urinary tract infections are one of the most frequent health problems and Uropathogenic Escherichia coli is the major pathogen resulting UTIs. The severity of UTIs is caused by the expression of a large range of virulence factors.In this study, we evaluated the allelic frequency fimH gene, in UPECs isolated from patients with UTIs. This study also aimed to determine the roles of C64...
متن کاملShould We Have Blind Faith in Bioinformatics Software? Illustrations from the SNAP Web-Based Tool
Bioinformatics tools have gained popularity in biology but little is known about their validity. We aimed to assess the early contribution of 415 single nucleotide polymorphisms (SNPs) associated with eight cardio-metabolic traits at the genome-wide significance level in adults in the Family Atherosclerosis Monitoring In earLY Life (FAMILY) birth cohort. We used the popular web-based tool SNAP ...
متن کامل