High-density microarrays can accommodate millions of oligonucleotide probes on a single microscopic glass slide. This great number of probes, when designed from the sequence of a genome, can cover the entire genome densely - with very small or no gap, or even overlapping in-between two probes adjacent to each other on the genome. The microarrays containing DNA probes designed to closely tile along an entire genomic sequence are called "genomic tiling microarrays". The coverage frequency depends on the size of the target genome and the number of probe spots on the microarray. The majority of microbial (both Bacteria and Archaea) genomes are smaller than 10 Mbp and can easily fit on a single high-density microarray with high-frequency probe coverage. Genomic tiling microarrays are thus ideal for studying the transcriptome, the complete collection of RNA transcribed in the cell, for most microbial genomes and can detect all types of RNA molecules including both protein-coding and non-coding RNA.
The goal of The Microbial Transcriptome Database (MTD) is to provide tools and information for studying the microbial transcriptome profiles, in particular the transcriptome data derived from the hybridization experiments using the high-density genomic tiling microarrays. Currently MTD provides a comprehensive and dynamic probe design pipeline for designing the genomic tiling array probe sets for all microbial genomic sequences. Probe sets for many microbial genomes can be downloaded and more genomes are being added to the probe design pipeline. MTD also accepts request for custom probe design with user specified genomes and array platforms. MTD also provides online tools and interfaces specifically designed for analyzing the transcriptome data.
MTD currently provides the following tools and information:
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| Dynamic Tiling Array Probe Design |
| * | Genomic Tiling Microarray Probe Sets
Download oligonucleotide DNA probes designed by the pipeline described in the article "Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays" (manuscript submitted) |
| * | Request Additional Custom Tiling Array Probe Sets
Due to the intense computation time for designing the probes using our pipeline, more probe sets will be gradually made available for all NCBI microbial genomes. If a probe set is not yet available, users can request for a particular genome to be designed in the next queue. We also accept requests for desiging probe sets with non-default parameters or for proprioety genomes. Please contact us for more detail. |
| Transcriptome profiling by HM-SVM |
| * | HM-SVM Algorithm
RNA expression signals detected by high-density genomic tiling microarrayscontain comprehensive transcriptome information of the target organism. Current methods for determining the RNA transcription units are still computer-intense and lack the discriminative power. HM-SVM is an efficient and accurate method for analyzing transcriptome profiles. (Manuscript submitted) |
| * | Download HM-SVM
Download HM-SVM script and sample microarray data |
| Microbial Transcriptome Profiles |
| * | Porphyromonas gingivalis W83 |
