GENOMEMASKER package for designing unique genomic PCR primers
Open Access
- 27 March 2006
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 7 (1), 172
- https://doi.org/10.1186/1471-2105-7-172
Abstract
Background The design of oligonucleotides and PCR primers for studying large genomes is complicated by the redundancy of sequences. The eukaryotic genomes are particularly difficult to study due to abundant repeats. The speed of most existing primer evaluation programs is not sufficient for large-scale experiments. Results In order to improve the efficiency and success rate of automatic primer/oligo design, we created a novel method which allows rapid masking of repeats in large sequence files, for example in eukaryotic genomes. It also allows the detection of all alternative binding sites of PCR primers and the prediction of PCR products. The new method was implemented in a collection of efficient programs, the GENOMEMASKER package. The performance of the programs was compared to other similar programs. We also modified the PRIMER3 program, to be able to design primers from lowercase-masked sequences. Conclusion The GENOMEMASKER package is able to mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10 000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.Keywords
This publication has 28 references indexed in Scilit:
- SNPbox: a modular software package for large-scale primer designBioinformatics, 2004
- Selection for 3′ end triplets for polymerase chain reaction primersMolecular and Cellular Probes, 2004
- Picky: oligo microarray design for large genomesBioinformatics, 2004
- Efficient selection of unique and popular oligos for large EST databasesBioinformatics, 2004
- me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elementsBioinformatics, 2004
- PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysisBioinformatics, 2002
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002
- A Greedy Algorithm for Aligning DNA SequencesJournal of Computational Biology, 2000
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Identification of common molecular subsequencesJournal of Molecular Biology, 1981