PROBer

PROBer is a software tool developed to design multiple primer pairs for generating PCR (polymerase chain reaction) probes beneficial for fluorescence in situ hybridization (FISH). The software application generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions. The TOPs are an alternative to bacterial artificial chromosomes (BACs) commonly used for FISH but have limitations like instability, unavailability, chimerism, or non-specificity to small genomic regions. The PROBer application can be used for any genomic locus that contains at least 10 kb of essentially unique blocks.

The software has been tested on several probes for genomic amplifications and hemizygous deletions that Representational Oligonucleotide Microarray Analysis of breast cancer tumors initially detected. The TOPs generated by PROBer can be amplified to yield small (100-2000 bp) DNA probes that will generate a single, strong fluorescent signal for regions as small as a single gene.

The availability of high-quality PCR probes is crucial for FISH experiments, and the PROBer software tool can design multiple primer pairs for generating PCR probes that are highly specific and effective in FISH experiments. The software is highly reliable and can be applied to any genomic locus that contains at least 10 kb of essentially unique blocks.

Topic

Nucleic acid structure analysis;Transcriptomics

Detail

  • Operation: Transcriptome assembly

  • Software interface: Command-line user interface

  • Language: R;Perl;Python

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 0.3.1

  • Credit: The National Institutes of Health (NIH), the Center for RNA Systems Biology at UC Berkeley.

  • Input: -

  • Output: -

  • Contact: lpachter@caltech.edu

  • Collection: -

  • Maturity: Stable

Publications

  • PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays.
  • Li B, et al. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. 2017; 4:568-574.e7. doi: 10.1016/j.cels.2017.04.007
  • https://doi.org/10.1016/j.cels.2017.04.007
  • PMID: 28501650
  • PMC: PMC5758053
  • PROBER: oligonucleotide FISH probe design software.
  • Navin N, et al. PROBER: oligonucleotide FISH probe design software. PROBER: oligonucleotide FISH probe design software. 2006; 22:2437-8. doi: 10.1093/bioinformatics/btl273
  • https://doi.org/10.1093/bioinformatics/btl273
  • PMID: 16740623
  • PMC: -

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