Oligodb--interactive design of oligo DNA for transcription profiling of human genes

Abstract

Motivation: The increasing use of customized oligo-DNA-microarrays has created a demand for convenient design of oligo nucleotides. The oligo-nucleotides have to serve as specific templates in the hybridization reaction.

Results: We have devised a web-based system for interactive design of suitable oligos for transcription profiling experiments with user-defined parameters. Oligodb is based on predicted human gene transcripts from the ENSEMBL project. The web interface allows the user to retrieve oligos for human transcripts in a flexible manner. Criteria for selecting the oligos are low similarity to all other known human genes, the absence of stable secondary structures, the length of the oligo, and the absence of low complexity regions. Furthermore, the user may select oligos corresponding to the desired position in the 5'-3' direction of the transcript, and based on the melting temperature. All data and results are tightly web-linked to the corresponding data entries of ENSEMBL project.