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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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DoriTool: A Bioinformatics Integrative Tool for Post-Association Functional Annotation.

Isabel Martín-Antoniano¹, Lola Alonso, Miguel Madrid

¹Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

Public Health Genomics

|July 13, 2017

Summary

DoriTool is a new bioinformatics pipeline that integrates various functional tools for in silico analysis. It simplifies variant annotation and interpretation, aiding researchers in understanding complex biological data.

Keywords:

Association Cancer Functional annotation Genome-wide association study Genomics Next-generation sequencing

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

High-throughput biological data necessitates advanced bioinformatics tools for functional analysis.
Existing tools often lack integration, increasing researcher workload and complexity.
Interpreting complex genomic data requires user-friendly, reproducible pipelines.

Purpose of the Study:

To present DoriTool, an integrated bioinformatics pipeline for functional in silico analysis.
To enhance reproducibility and reduce research time, particularly for users with limited bioinformatics expertise.
To aid in the interpretation of biologically meaningful data from variant annotation.

Main Methods:

DoriTool employs a modular design and integrative strategy using Bash, Perl, and R scripts.
It performs functional annotation at multiple levels: mutation/variant, gene, pathway, and network.
The pipeline integrates up-to-date functional and genomic data, including third-party tools and Genotype-Tissue Expression (GTEx) data.

Main Results:

DoriTool provides comprehensive variant annotation, gene annotation, and pathway analysis.
Visual reports include linkage disequilibrium proxies, GTEx eQTL results, and colored pathways.
Application to prostate cancer-associated variants demonstrates its utility in biological interpretation.

Conclusions:

DoriTool is a comprehensive and user-friendly bioinformatics tool for functional in silico annotation of variants.
It significantly aids researchers in interpreting genetic associations and understanding underlying biological mechanisms.
The tool is publicly available with code, documentation, and a GitHub repository.