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A computer program for the design of optimal synthetic oligonucleotide probes for protein coding genes
A Danckaert1, C Mugnier, P Dessen
1CITI 2, Paris, France.
Computer Applications in the Biosciences : CABIOS
|November 1, 1987
Summary
A new computer program designs artificial oligonucleotide probes for molecular cloning by identifying optimal protein sequence regions. It also checks for homology against nucleotide databases and minimizes probe degeneracy.
Area of Science:
- Bioinformatics
- Molecular Biology
- Computational Biology
Background:
- Designing effective oligonucleotide probes is crucial for molecular cloning and genetic analysis.
- Identifying suitable target sequences with minimal degeneracy is a key challenge in probe design.
Purpose of the Study:
- To develop a computational tool for designing artificial oligonucleotide probes with optimal length and limited degeneracy.
- To enable efficient screening of protein sequences for probe design and homology checking against nucleotide databases.
Main Methods:
- A FORTRAN 77 computer program was developed.
- The program analyzes protein sequences to find regions suitable for probe design.
- It incorporates options to eliminate rare codons and optimize base selection to reduce probe degeneracy.
- Homology searches against nucleotide sequence databases are performed.
Main Results:
- The program successfully identifies protein sequence regions for designing oligonucleotide probes.
- It provides options to control probe degeneracy by codon and base selection.
- Homology checks against existing sequence data are integrated.
Conclusions:
- This computational approach facilitates the design of specific and efficient oligonucleotide probes.
- The program aids in minimizing potential issues arising from probe degeneracy and off-target binding.
- It serves as a valuable tool for molecular cloning and related genetic research applications.