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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.

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Related Experiment Video

Updated: Jun 12, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Accessing the SEED genome databases via Web services API: tools for programmers.

Terry Disz¹, Sajia Akhter, Daniel Cuevas

¹Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.

BMC Bioinformatics

|June 16, 2010

Summary

This summary is machine-generated.

The SEED database now offers a robust API via Web services, providing efficient programmatic access to microbial genome annotations. This allows for timely retrieval of the latest genomic data without large downloads.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

The SEED integrates public genome sequences into a unified resource.
It employs the subsystems concept for accurate microbial genome annotation.
The SEED backend supports tools like the Rapid Annotation using Subsystems Technology (RAST) server.

Purpose of the Study:

To introduce a novel method for accessing the SEED database.
To provide programmatic access to genomics data through a Web services API.

Main Methods:

Development and deployment of Web services for the SEED database.
Utilizing a platform-independent, service-oriented architecture.
Providing example code for accessing data using common programming languages (Perl, Python, Java).

Main Results:

Over forty Web service methods are available for accessing microbial genome annotation data.
Web services offer comprehensive and consistent access to the SEED database backend.
Programmatic access enables developers to build third-party tools and mash-ups.

Conclusions:

A novel Web services API provides robust access to the SEED database.
This approach facilitates timely access to current genomic datasets.
It eliminates the need for large, single-instance data downloads.