With the fast expansion of DNA and protein databases in recent years, the design of oligonucleotides based on these databases has become important for molecular biologists. In particular the databases of gene seqeunces can be used to design degenerate oligonucleotides based on groups of related genes (or families) in the databases. The degenerate oligonucelotides are commonly used to discover new family members in experimental conditions.
The designed oligonucleotides can be easily synthesized and used as hybridization probes as well as Polymerase Chain Reaction (PCR) primers. However, designing oligonucleotides is not easy to do manually especially when large number of oligonucleotides for many gene families are needed. For example, DNA microarrays which can detect thousands of genes in parallel, need thousands of oligonucleotides to attach on microarry chips.
To help design oligonucleotides many computer programmers have been writing oligonucleotide design programs. Some of these programs can be used on the internet and are provided without cost. However, one of the biggest obstacles to use these programs is a lack of integration. To design oligonucleotides and examine homology to known sequences requires the use of multiple programs running on different computer platforms, and extensive manual reformatting of data between applications.
This has lead to the development of the DEgenerate Oligonucleotide Design and Analysis System (DEODAS). DEODAS integrates existing programs and automates the process of oligonucleotide design for multiple protein families. Oligonucleotides for protein families can be designed in large batches. This allows the researcher to set up the program to design oligonucleotdes for any number of protein families and let the computer do the work by itself. This greatly cuts down on interactive work time.
In addition DEODAS adds features to the design process to aid in producing and selecting high quality oligonucleotides. The program divides dissimilar sequences into subfamilies and produces oligonucleotides targeted to the specific subfamily instead of the whole, making more specifically targeted oligonucleotides. The designed oligonucleotides are automatically screened against gene databases for homology. Through this screening process the oligonucleotides are comfired against the gene sequences they were designed from and checked for the possibility of cross-hybridization to unrelated sequences. The design and screening results are automatically stored in a searchable database. This database can be analyzed interactively by the researcher giving the researcher control over which oligonucleotides are selected for use.
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