The Aldehyde Dehydrogenase Gene Superfamily Resource Center

William Black,Vasilis Vasiliou

doi:10.1186/1479-7364-4-2-136

Abstract

The website http://www.aldh.org is a publicly available database for nomenclature and functional and molecular sequence information for members of the aldehyde dehydrogenase (ALDH) gene superfamily for animals, plants, fungi and bacteria. The site has organised gene-specific records. It provides synopses of ALDH gene records, marries trivial terms to correct nomenclature and links global accession identifiers with source data. Server-side alignment software characterises the integrity of each sequence relative to the latest genomic assembly and provides identifier-specific detail reports, including a graphical presentation of the transcript's exon - intron structure, its size, coding sequence, genomic strand and locus. Also included are a summary of substrates, inhibitors and enzyme kinetics. The site provides reference lists and is designed to facilitate data mining by interested investigators.

Highlights

The completion of various genome projects and the growing trend towards high-throughput data production have created a significant knowledge base of molecular sequence data across a broad spectrum of species
Other issues include lack of identification and/or categorisation of alternatively spliced transcriptional variants, as well as erroneous functional characterisations because generalised gene ontology entries do not distinguish the individual gene from other members of its gene superfamily
We have developed a genespecific database architecture and web-based scripting system which is tailored to report both the molecular sequence and functional data for all members of an individual gene superfamily across all species (Black and Vasiliou, manuscript in preparation)

Summary

Introduction

The completion of various genome projects and the growing trend towards high-throughput data production have created a significant knowledge base of molecular sequence data across a broad spectrum of species. Other issues include lack of identification and/or categorisation of alternatively spliced transcriptional variants, as well as erroneous functional characterisations because generalised gene ontology entries do not distinguish the individual gene from other members of its gene superfamily To address these limitations, we have developed a genespecific database architecture and web-based scripting system which is tailored to report both the molecular sequence and functional data for all members of an individual gene superfamily across all species (Black and Vasiliou, manuscript in preparation). We have developed a genespecific database architecture and web-based scripting system which is tailored to report both the molecular sequence and functional data for all members of an individual gene superfamily across all species (Black and Vasiliou, manuscript in preparation) Using this software and relational database architecture, we have developed www.aldh.org, a publicly available. The site database operates on the open-source database software MySQL (version 5.0.51a) and content is dynamically generated via server-side scripting using the open-source script engine, PHP (version 5.2.9-2)

Organisation of the web database

Black and Vasiliou

Data mining and processing

Future directions