Dataset Information

Genomorama: genome visualization and analysis.

ABSTRACT: BACKGROUND: The ability to visualize genomic features and design experimental assays that can target specific regions of a genome is essential for modern biology. To assist in these tasks, we present Genomorama, a software program for interactively displaying multiple genomes and identifying potential DNA hybridization sites for assay design. RESULTS: Useful features of Genomorama include genome search by DNA hybridization (probe binding and PCR amplification), efficient multi-scale display and manipulation of multiple genomes, support for many genome file types and the ability to search for and retrieve data from the National Center for Biotechnology Information (NCBI) Entrez server. CONCLUSION: Genomorama provides an efficient computational platform for visualizing and analyzing multiple genomes.

SUBMITTER: Gans JD

PROVIDER: S-EPMC1906841 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genomorama: genome visualization and analysis.

Gans Jason D JD Wolinsky Murray M

BMC bioinformatics 20070614

<h4>Background</h4>The ability to visualize genomic features and design experimental assays that can target specific regions of a genome is essential for modern biology. To assist in these tasks, we present Genomorama, a software program for interactively displaying multiple genomes and identifying potential DNA hybridization sites for assay design.<h4>Results</h4>Useful features of Genomorama include genome search by DNA hybridization (probe binding and PCR amplification), efficient multi-scale ...[more]

PMID: 17570856

Similar Datasets

Project description:BackgroundThousands of research studies concerning genome-wide association studies (GWAS) in Alzheimer's disease (AD) have been published in the last decades. However, a comprehensive understanding of the current research status and future development trends of GWAS in AD have not been clearly shown. In this study, we tried to gain a systematic overview of GWAS in AD by bibliometric and visualization analysis.MethodsThe literature search terms are: ("genome-wide analysis" or "genome-wide association study" or "whole-genome analysis") AND ("Alzheimer's Disease" or "Alzheimer Disease"). Relevant publications were extracted from the Web of Science Core Collection (WoSCC) database. Collected data were further analyzed using VOSviewer, CiteSpace and R package Bibliometrix. The countries, institutions, authors and scholar collaborations were investigated. The co-citation analysis of publications was visualized. In addition, research hotspots and fronts were examined.ResultsA total of 1,350 publications with 59,818 citations were identified. The number of publications and citations presented a significant rising trend since 2013. The United States was the leading country with an overwhelming number of publications (775) and citations (42,237). The University of Washington and Harvard University were the most prolific institutions with 101 publications each. Bennett DA was the most influential researcher with the highest local H-index. Neurobiology of Aging was the journal with the highest number of publications. Aβ, tau, immunity, microglia and DNA methylation were research hotspots. Disease and causal variants were research fronts.ConclusionThe most frequently studied AD pathogenesis and research hotspots are (1) Aβ and tau, (2) immunity and microglia, with TREM2 as a potential immunotherapy target, and (3) DNA methylation. The research fronts are (1) looking for genetic similarities between AD and other neurological diseases and syndromes, and (2) searching for causal variants of AD. These hotspots suggest noteworthy directions for future studies on AD pathogenesis and genetics, in which basic research regarding immunity is promising for clinical conversion. The current under-researched directions are (1) GWAS in AD biomarkers based on large sample sizes, (2) studies of causal variants of AD, and (3) GWAS in AD based on non-European populations, which need to be strengthened in the future.

Dataset Information

Genomorama: genome visualization and analysis.

Publications

Genomorama: genome visualization and analysis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets