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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Reporting and recording are crucial in data documentation. The timely, thorough, and accurate documentation of facts is essential when recording patient data. Failure to record findings during an assessment or interpretation of a problem will result in loss of information and make the patient document unreliable. The reader is left with general impressions if the information is not specific. A recording is documenting data of the individual's health information in a traceable, secure, and...

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

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dictyBase 2015: Expanding data and annotations in a new software environment.

Siddhartha Basu¹, Petra Fey¹, David Jimenez-Morales¹

¹dictyBase, Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, 750 N. Lake Shore Drive, Chicago, IL 60611, USA.

Genesis (New York, N.Y. : 2000)

|June 20, 2015

Summary

dictyBase provides integrated data and tools for Dictyostelium discoideum research. This model organism database offers comprehensive gene annotations, strain information, and advanced comparative genomics, supporting the biomedical community.

Keywords:

Chado Dictyostelium Gene Ontology annotations phenotypes relational database

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Published on: January 15, 2020

Area of Science:

* Molecular Biology
* Genomics
* Bioinformatics

Background:

* dictyBase serves as the primary model organism database for Dictyostelium discoideum.
* The biomedical research community requires integrated, high-quality data and tools for effective research.

Purpose of the Study:

* To provide the biomedical research community with well-integrated, high-quality data and tools for Dictyostelium discoideum.
* To enhance data accessibility and research capabilities through infrastructure upgrades and innovative tools.

Main Methods:

* Data acquisition from sequencing centers and high-throughput experiments (mutagenesis, RNAseq).
* Manual curation of functional gene annotations, including Gene Ontology, strain, and phenotype data.
* Infrastructure overhaul to support advanced tools and comparative genomics.

Main Results:

* Comprehensive integration of diverse data types including sequencing, functional annotations, and stock information.
* Implementation of innovative tools and comparative genomics capabilities.
* Improved data quality and accessibility for researchers.

Conclusions:

* dictyBase is a trusted resource for Dictyostelium discoideum research, supporting investigators, organizations, and educators.
* Recent upgrades enhance the database's utility for bench researchers and facilitate the use of rapidly increasing data volumes.
* The database fosters a collaborative relationship with the research community, ensuring responsiveness to user needs.