Abstract
Modern molecular biology has rapidly sophisticated in the last years. Whereas in former times researchers in a lab worked on one or few genes only, today we process thousands of genes in a while. These high-throughput methods produce large amount of information, which needs to be handled in appropriate way. Therefore, a new data managing approach is needed. This often requires developing of software adapted to the specific needs of the scientists.
Here I present two software tools, which implementation was inspired by the practice in the lab.
PrimerFactory can be used to query a DNA sequence for matches in an oligonucleotide-database. This, among other benefits, allows the researchers to reuse their existing oligonucleotide stocks. In addition, this tool supports primer design in a batch mode by using Primer3 core.
RNAi (RNA interference) is a new method for gene-specific suppression of the expression. A major weakness of the method is the miss targeting of unrelated genes. The second tool (yet nameless) scans the RNAi triggering sequence for putative off-targets in a customizable nucleotide sequence database.
These examples aim to show the broadness and in the same time the specificit of tasks that can be addressed to the bioinformatics today.
Here I present two software tools, which implementation was inspired by the practice in the lab.
PrimerFactory can be used to query a DNA sequence for matches in an oligonucleotide-database. This, among other benefits, allows the researchers to reuse their existing oligonucleotide stocks. In addition, this tool supports primer design in a batch mode by using Primer3 core.
RNAi (RNA interference) is a new method for gene-specific suppression of the expression. A major weakness of the method is the miss targeting of unrelated genes. The second tool (yet nameless) scans the RNAi triggering sequence for putative off-targets in a customizable nucleotide sequence database.
These examples aim to show the broadness and in the same time the specificit of tasks that can be addressed to the bioinformatics today.