In silico Reconstruction of the Metabolic and Pathogenic Potential of Bacterial Genomes Using Subsystems

2009 ◽  
pp. 21-34 ◽  
Author(s):  
L.K. McNeil ◽  
R.K. Aziz
Keyword(s):  
In Silico ◽  
Bacterial Genomes ◽  
Pathogenic Potential

scholarly journals THE IN SILICO PREDICTION OF PROMOTERS IN BACTERIAL GENOMES

2007 ◽  
Author(s):  
MICHAEL TOWSEY ◽  
JAMES M. HOGAN ◽  
SARAH MATHEWS ◽  
PETER TIMMS
Keyword(s):  
In Silico ◽  
In Silico Prediction ◽  
Bacterial Genomes

scholarly journals mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes

2010 ◽  
Vol 38 (suppl_2) ◽  
pp. W194-W200 ◽  
Author(s):  
Yucheng Shao ◽  
Xinyi He ◽  
Ewan M. Harrison ◽  
Cui Tai ◽  
Hong-Yu Ou ◽  
...  
Keyword(s):  
In Silico ◽  
Subtractive Hybridization ◽  
Hybridization Analysis ◽  
Bacterial Genomes ◽  
Web Based

scholarly journals In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction

2004 ◽  
Vol 20 (5) ◽  
pp. 798-799 ◽  
Author(s):  
J. Bikandi ◽  
R. S. Millan ◽  
A. Rementeria ◽  
J. Garaizar
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Bacterial Genomes ◽  
Silico Analysis

scholarly journals Analysis of variators in the brca1 and brca2 genes by ngs in patients from central brazil with suspected hboc syndrome: a new pathogenic variant identified

Mastology ◽  
2020 ◽  
Vol 30 (Suppl 1) ◽  
Author(s):  
Rebeca Mota Goveia ◽  
Paula Francinete Faustino da Silva ◽  
Thais Bomfim Teixeira ◽  
Ruffo de Freitas ◽  
Elisângela de Paula Silveira Lacerda
Keyword(s):  
At Risk ◽  
In Silico ◽  
Brca2 Gene ◽  
Brca1 Gene ◽  
Published Data ◽  
Brca1 And Brca2 ◽  
Pathogenic Potential ◽  
Pathogenic Variants ◽  
Brca1 And Brca2 Genes ◽  
Patients At Risk

About 10‒15% of breast cancer cases are due to deleterious germ changes, more than half of which are located in the BRCA1 or BRCA2 genes. The screening of variants in these genes for patients at risk brings benefits for better clinical management of the patient as well as for the prevention of disease recurrences both in the proband and in their relatives. The profile of genetic variants is little known to the Brazilian population and, to date, there are no published data for the population of the central region of the country. This study aimed to analyze the profile of pathogenic variants (VP) and of uncertain significance (VUS) in the BRCA1 and BRCA2 genes in this population. We selected 102 patients seen at Hospital das Clínicas, Universidade Federal de Goiás, with clinical diagnosis of invasive ductal carcinoma that met the criteria of the National Comprehensive Cancer Networking 2016/2 for hereditary breast and ovarian cancer syndrome. A collection of 4mL of peripheral blood was carried out and submitted to subsequent extraction of genomic DNA, carried out using the PureLink kit (Invitrogen). The genes in question had all their exon-intron regions sequenced using the MiSeq device (Illumina) and the raw data were evaluated using the Sophia DDM software. The risk of in silico pathogenicity of the VUS was analyzed by the software POLYPHEN2, MutationTaster, SIFT, ESP5400, G1000, GnomAD. Of the total of 102 patients evaluated in this study, 22 (21.56%) had PV or VUS in the BRCA1 or BRCA2 genes. Of these, 16 patients (72.81%) had pathogenic variants, eight with PV in BRCA1 (c.5266dupC (2), c.3331_3334delCAAC, c.211A>G, c.3228_3229delAG, c.3700_3704delGTAAA, c.4484G>T and c.5305_5306ins20) and eight with PV in BRCA2 (c.156_157insAlu, c.4829_4830delTG, c.8488-1G>A, c.6405_6409delCTTAA (3), c.517-1G>A, c.2808_2811delACAA). A total of 7 patients (31.8%) presented VUS in these genes, one in the BRCA1 gene (c.179A>G) and five in the BRCA2 gene (c.280C>T, c.811G>A, 1096T>G, 1441A>G and c.5270A>G) of which only the variant c.1441A>G had low pathogenic potential in silico. A new PV still not described in the literature was also identified, variant c.5305_5306ins20 in the BRCA1 gene. These data suggest that all patients at risk in this population should be evaluated for PV or VUS in the BRCA1 and BRCA2 genes since the presence of these variants can help in the patient's prognosis and disease prevention.

scholarly journals The In Silico Genotyper (ISG): an open-source pipeline to rapidly identify and annotate nucleotide variants for comparative genomics applications

2015 ◽  
Author(s):  
Jason W Sahl ◽  
Stephen M Beckstrom-Sternberg ◽  
James Babic-Sternberg ◽  
John D Gillece ◽  
Crystal M Hepp ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Open Source ◽  
In Silico ◽  
Sequence Data ◽  
Source Code ◽  
Whole Genome Sequence ◽  
Nucleotide Polymorphisms ◽  
Bacterial Genomes ◽  
Single Nucleotide ◽  
General Public License

The identification and annotation of nucleotide variants, including insertions/deletions and single nucleotide polymorphisms (SNPs), from whole genome sequence data is important for studies of bacterial evolution, comparative genomics, and phylogeography. The in silico Genotyper (ISG) represents a parallel, tested, open source tool that can perform these functions and scales well to thousands of bacterial genomes. ISG is written in Java and requires MUMmer (Delcher, et al., 2003), BWA (Li and Durbin, 2009), and GATK (McKenna, et al., 2010) for full functionality. The source code and compiled binaries are freely available from https://github.com/TGenNorth/ISGPipeline under a GNU General Public License. Benchmark comparisons demonstrate that ISG is faster and more flexible than comparable tools.

scholarly journals In vivo and in silico Virulence Analysis of Leptospira Species Isolated From Environments and Rodents in Leptospirosis Outbreak Areas in Malaysia

2021 ◽  
Vol 12 ◽  
Author(s):  
Noraini Philip ◽  
Jaeyres Jani ◽  
Nurul Natasya Azhari ◽  
Zamberi Sekawi ◽  
Vasantha Kumari Neela
Keyword(s):  
In Silico ◽  
Fatal Outcome ◽  
Clinical Manifestations ◽  
Epidemiological Surveillance ◽  
Pathogenic Species ◽  
Pathogenic Potential ◽  
Virulence Analysis ◽  
Outbreak Areas ◽  
The Difference

The zoonotic disease leptospirosis is caused by pathogenic species of the genus Leptospira. With the advancement of studies in leptospirosis, several new species are being reported. It has always been a query, whether Leptospira species, serovars, and strains isolated from different geographical locations contribute to the difference in the disease presentations and severity. In an epidemiological surveillance study performed in Malaysia, we isolated seven novel intermediate and saprophytic species (Leptospira semungkisensis, Leptospira fletcheri, Leptospira langatensis, Leptospira selangorensis, Leptospira jelokensis, Leptospira perdikensis, Leptospira congkakensis) from environments and three pathogenic species from rodents (Leptospira borgpetersenii strain HP364, Leptospira weilii strain SC295, Leptospira interrogans strain HP358) trapped in human leptospirosis outbreak premises. To evaluate the pathogenic potential of these isolates, we performed an in vivo and in silico virulence analysis. Environmental isolates and strain HP364 did not induce any clinical manifestations in hamsters. Strain SC295 caused inactivity and weight loss with histopathological changes in kidneys, however, all hamsters survived until the end of the experiment. Strain HP358 showed a high virulent phenotype as all infected hamsters died or were moribund within 7 days postinfection. Lungs, liver, and kidneys showed pathological changes with hemorrhage as the main presentation. In silico analysis elucidated the genome size of strain HP358 to be larger than strains HP364 and SC295 and containing virulence genes reported in Leptospira species and a high number of specific putative virulence factors. In conclusion, L. interrogans strain HP358 was highly pathogenic with fatal outcome. The constituent of Leptospira genomes may determine the level of disease severity and that needs further investigations.

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