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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

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WebGMAP: a web service for mapping and aligning cDNA sequences to genomes.

Chun Liang¹, Lin Liu, Guoli Ji

¹Department of Botany, Department of Computer Science and Systems Analysis, Miami University, Oxford, OH 45056, USA. liangc@muohio.edu

Nucleic Acids Research

|May 26, 2009

Summary

WebGMAP is a new web service that makes genomic data accessible for biologists. It integrates tools for cDNA-genome alignment and visualization, aiding in gene structure analysis and discovery of variations.

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Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Thousands of organism genomes are being sequenced, generating vast amounts of data.
Making genomic sequences and annotations user-friendly for biologists is a significant challenge.

Purpose of the Study:

To develop an accessible web service for analyzing genomic data.
To facilitate genome annotation improvement, gene structure determination, and exploration of biological processes.
To enable discovery of genetic variations through cDNA-genome alignments.

Main Methods:

Developed WebGMAP, an open-access web service integrating cDNA-genome alignment tools (e.g., GMAP) with visualization and data mining functionalities.
Implemented a web-based sequence viewer with functions like nucleotide positioning, six-frame translations, and motif detection.
Integrated an EST-Genome-Browser for displaying gene structures and alignments, highlighting base differences.

Main Results:

WebGMAP provides seamless integration of alignment and visualization tools.
The service offers routine sequence analysis functions and data filtering/searching capabilities.
The EST-Genome-Browser effectively displays gene structures and alignments, aiding in the identification of potential genetic variations.

Conclusions:

WebGMAP enhances accessibility of genomic data for general biologists.
The tool supports community efforts in improving genome annotation and understanding gene structures.
WebGMAP facilitates the discovery of genetic variations by analyzing cDNA-genome alignments.