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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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AnnotateGenomicRegions: a web application.

Luca Zammataro, Rita DeMolfetta, Gabriele Bucci

BMC Bioinformatics

|February 26, 2014

Summary

This summary is machine-generated.

AnnotateGenomicRegions is a new, open-source web application simplifying genomic region annotation. This tool assists biologists and bioinformaticians in interpreting large genomic datasets without requiring extensive bioinformatics expertise.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Modern genomic technologies generate vast amounts of data requiring mapping to specific genomic regions.
Interpreting genomic data necessitates annotating regions with known features like genes and promoters.
Existing annotation tools often demand significant bioinformatics skills or software installation.

Purpose of the Study:

To present AnnotateGenomicRegions, a user-friendly web application for annotating genomic regions.
To provide an accessible tool for biologists and bioinformaticians to interpret genomic data.

Main Methods:

Developed a web application accepting genomic regions as input.
Integrated support for multiple organisms and genome builds (human, mouse, zebrafish, yeast).
Enabled online accessibility and local installation, with options for embedded and custom annotations.

Main Results:

AnnotateGenomicRegions provides overlapping and neighboring genome annotations for user-defined regions.
The application supports human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and yeast (sacCer2, sacCer3).
Users can utilize embedded annotations or add custom ones, with options for online or local use.

Conclusions:

AnnotateGenomicRegions addresses the need for a simple, accessible genomic region annotation tool.
The open-source web application is easily installable on personal computers or servers.
Facilitates genomic data interpretation for both biologists and bioinformaticians.