OligoSpawn: a software tool for the design of overgo probes from large unigene datasets

BACKGROUND: Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the design of overlapping oligonucleotide (overgo) probes from large unigene (EST-contigs) datasets. RESULTS: OLIGOSPAWN is a suite of software tools that offers two complementary services, namely (1) the selection of "unique" oligos each of which appears in one unigene but does not occur (exactly or approximately) in any other and (2) the selection of "popular" oligos each of which occurs (exactly or approximately) in as many unigenes as possible. In this paper, we describe the functionalities of OLIGOSPAWN and the computational methods it employs, and we report on experimental results for the overgo probes designed with it. CONCLUSION: The algorithms we designed are highly efficient and capable of processing unigene datasets of sizes on the order of several tens of Mb in a few hours on a regular PC. The software has been used to design overgo probes employed to screen a barley BAC library (Hordeum vulgare). OLIGOSPAWN is freely available at

A comparative analysis of existing oligonucleotides selection algorithms for microarray technology

In system biology, DNA microarray technology is an indispensable tool for the biological analysis involved at the level of the whole genome. Among the sophisticated analytical problems in microarray technology at the front and back ends, respectively, are the selection of optimal DNA oligonucleotides (henceforth oligos) and computational analysis of the genes expression data. A computational comparative analysis of the methods used to select oligos is important since the design and quality of the microarray probes are of critical importance for the hybridization experiments as well as subsequent analysis of the data. In an attempt to enhance efficient and effective design at the front end, a computational comparative analysis was performed on oligos selection tools using the barley ESTs, as well as the Saccharomyces cerevisiae, Encephalitozoon cuniculi and human genomes. The analysis also shows that a large number of the existing tools are difficult to install and configure. For cross hybridization test, most rely on BLAST and therefore design ill specific oligonucleotides. Furthermore, most are non-intuitive to use and lack important oligo design and software features

A comparative analysis of existing oligonucleotides selection algorithms for microarray technology

In system biology, DNA microarray technology is an indispensable tool for the biological analysis involved at the level of the whole genome. Among the sophisticated analytical problems in microarraytechnology at the front and back ends, respectively, are the selection of optimal DNA oligonucleotides (henceforth oligos) and computational analysis of the genes expression data. A computational comparative analysis of the methods used to select oligos is important since the design and quality of the microarray probes are of critical importance for the hybridization experiments as well as subsequent analysis of the data. In an attempt to enhance efficient and effective design at the front end, a computational comparative analysis was performed on oligos selection tools using the barley ESTs, as well as the Saccharomyces cerevisiae, Encephalitozoon cuniculi and human genomes. The analysis also shows that a large number of the existing tools are difficult to install and configure. For cross hybridization test, most rely on BLAST and therefore design ill specific oligonucleotides. Furthermore,most are non-intuitive to use and lack important oligo design and software features

GENOMEMASKER package for designing unique genomic PCR primers

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

Efficient Selection of Unique and Popular Oligos For Large EST databases

EST databases have grown exponentially in recent years and now represent the largest collection of genetic sequences. An important application of these databases is that they contain information useful for the design of gene-specific oligonucleotides (or simply, oligos) that can be used in PCR primer design, microarray experiments, and genomic library screening. In this paper, we study two complementary problems concerning the selection of short oligos, e.g., 20--50 bases, from a large database of tens of thousands of EST sequences: (i) selection of oligos each of which appears (exactly) in one EST sequence but does not appear (exactly or approximately) in any other EST sequence and (ii) selection of oligos that appear (exactly or approximately) in many ESTs. The first problem is called the unique oligo problem and has applications in PCR primer and microarray probe designs. The second is called the popular oligo problem and is useful in screening genomic libraries (such as BAC libraries) for gene-rich regions. We present an e#cient algorithm to identify all unique oligos in the ESTs and an e#cient heuristic algorithm to enumerate the most popular oligos. By taking into account the distribution of the frequencies of the words in the EST database, the algorithms have been carefully engineered to achieve remarkable running times on regular PCs. Each of the algorithms takes only a couple of hours (on a 1.2 GHz CPU, 1 GB RAM machine) to run on a dataset 28 Mbases of barley ESTs from the HarvEST database. We present simulation results on synthetic data and a preliminary analysis of the barley EST database