The aldehyde dehydrogenase gene superfamily resource center

Abstract

The website 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.

Figure 1

Alternatively spliced transcriptional variants for the ALDH gene superfamily member, ALDH3A1. The graphical representations for transcriptional variants for each gene superfamily member are dynamically generated based on sequences from each accession identifier and represent the splice variants for a particular gene and species, thereby allowing users quickly to identify similarities and differences between all available splice variants.

Figure 2

Graphical representation of the transcript sequence for individual accession identifiers. Each accession identifier's sequence within the database is analysed for inter- and intra-sequence structure. Data from this analysis is then parsed and graphically represented for each accession identifier in the 'Accession Identifier Detail Reports' section found under Molecular Features for each gene record. If present, any variations in the transcript sequence as a result of synonymous and non-synonymous polymorphisms relative to the genomic sequence are highlighted.

Figure 3

Graphical representation of the peptide sequence for individual accession identifiers. Peptide translation for each transcript sequence is represented by a multicoloured graphic of the primary sequence based on amino acid content (Figure 3a). If present, any variations in amino acids as a result of synonymous and non-synonymous polymorphisms relative to the genomic sequence are highlighted. In addition, users are able to view the locations of various residues within the peptide sequence (eg cysteine residues; Figure 3b) by clicking on a specific residue in the amino acid content table of Figure 3a.

Figure 4

Data mining and processing for www.aldh.org. Site administrators collect specific data elements from major database repositories in the form of site-generated XML documents. These XML documents are then incorporated, parsed and inserted into the www.aldh.org database architecture by the server-side administrative script engines. The newly inserted data are then readily available for web server processing and display to the public.