[Genome] custom scripting for probe design

[rbelc001@student.ucr.edu]

I'm in the process of making 25-mer probes for biodegradation gene identification, but I first need a custom script that can identify ortholog clusters based on several FASTA formatted sequences that are aligned; identifying conserved areas and generating a single sequence to represent the many aligned and conserved sequences. Is anyone aware of a custom script that can perform such a function? It is important to note that this is for probe design, and NOT for primer design.
Richard