Tool for Design of DNA Microarray Probes
Tool for Oligonucleotide Identification - TOFI

TOFI - (Tool for Oligonucleotide Identification) is a bioinformatics tool that allows biologists to identify in silico genomic fingerprints for the design of microarray-based pathogen diagnostic assays. The algorithm implemented in TOFI consists of three steps. First, it compares the target genome with one or more biological near-neighbor genomes and identifies candidate sequences, i.e., those subsequences of the target genome that are not present in the near-neighbor genome, using the suffix tree-based software MUMmer [1]. Second, DNA probes that satisfy experimental constraints, such as length, melting temperature, and GC content from the candidate sequences using the commercial software Oligonucleotide Modeling Platform (OMP)[2]. An open-source alternative to OMP based on the UNAfold software [3] is also available. Finally, TOFI quantifies the specificity of each DNA probe by examining the best alignments produced by BLAST [4] and comparing them against a set of specificity criteria. The TOFI pipeline:

  • Employs parallelized software using MPI.
  • Is capable of identifying fingerprints for a bacterial genome by comparing it to a near-neighbor in ~5 hours. [5,6]
  • Is currently available at the Army Research Laboratory Major Shared Resource Center on the mjm 4400 cores Linux cluster.
  • Has the ability to identify DNA fingerprints that are common to a group of pathogens, while being unique with respect to any other genome.
  • Is capable of designing fingerprints for viral genomes.
  • Is easily accessible through its Web-based graphic user interface (GUI) using the User Interface Toolkit (UIT).
      

[1]Kurtz A, Phillippy AL, Delcher M, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biology. 2004 Jan 30;5:R12.
[2]Available at www.dnasoftware.com.
[3]Available at www.bioinfo.rpi.edu/applications/hybrid/man/UNAFold.php.
[4]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology. 1990 Oct 5;215:403.
[5]Tembe, W., N. Zavaljevski, E. Bode, C. Chase, J. Geyer, L. Wasieloski, G. Benson, and J. Reifman. Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics. 2007 January 1; 23(1):5-13.
[6]Vijaya Satya, R., N. Zavaljevski, K. Kumar, and J. Reifman. A high-throughput pipeline for designing microarray-based pathogen diagnostic assays. BMC Bioinformatics. 2008 April 12; 9:185.
Planned Upgrades
  • Modules to design PCR-based diagnostic assays
Publications
Vijaya Satya, R., N. Zavaljevski, K. Kumar, E. Bode, S. Padilla, L. Wasieloski, J. Geyer, and J. Reifman. In silico microarray probe design for diagnosis of multiple pathogens. BMC Genomics. 2008 October 21; 9:496. [PDF]
Tembe, W., N. Zavaljevski, E. Bode, C. Chase, J. Geyer, L. Wasieloski, G. Benson, and J. Reifman. Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics. 2007 January 1; 23(1):5-13. [PDF]
Vijaya Satya, R., N. Zavaljevski, K. Kumar, and J. Reifman. A high-throughput pipeline for designing microarray-based pathogen diagnostic assays. BMC Bioinformatics. 2008 April 12; 9:185. [PDF]