Abstract
The non-coding fraction of the human genome, which is approximately 98%, is mainly constituted by repeats. Transpositions, expansions and deletions of these repeat elements contribute to a number of diseases. None of the available databases consolidates information on both tandem and interspersed repeats with the flexibility of FASTA based homology search with reference to disease genes. Repeats in diseases database (RiDs db) is a web accessible relational database, which aids analysis of repeats associated with Mendelian disorders. It is a repository of disease genes, which can be searched by FASTA program or by limitedor free- text keywords. Unlike other databases, RiDs db contains the sequences of these genes with access to corresponding information on both interspersed and tandem repeats contained within them, on a unified platform. Comparative analysis of novel or patient sequences with the reference sequences in RiDs db using FASTA search will indicate change in structure of repeats, if any, with a particular disorder. This database also provides links to orthologs in model organisms such as zebrafish, mouse and Drosophila. The database is available for free at http://115.111.90.196/ridsdb/index.php.
Highlights
The complexity of mammalian genomes is compounded by the presence of large number of repetitive elements whose functions have not yet been fully deciphered
Transpogene [7] covers transposable elements located inside protein coding genes of seven species including human genome with no option for searching either by disease or repeat-related information
Implementation: Repeats in diseases database (RiDs db) is a relational database with well-defined schema and has been implemented using the Structured Query Language (SQL) from the MySQL server version 5.1
Summary
The complexity of mammalian genomes is compounded by the presence of large number of repetitive elements whose functions have not yet been fully deciphered. Depending on their distribution within the genomes, repeat sequences can be divided into tandemly arrayed and interspersed repeats Aberrant transpositions of these repeats contribute to number of diseases such as cholinesterase deficiency, Ehlers-Danlose. Satellog [6] is another database that describes tandem repeats in disease genes with the option of obtaining OMIM IDs. Transpogene [7] covers transposable elements located inside protein coding genes of seven species including human genome with no option for searching either by disease or repeat-related information. Transpogene [7] covers transposable elements located inside protein coding genes of seven species including human genome with no option for searching either by disease or repeat-related information None of these contain options for a homology-based search.
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