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CloneTools of OFRG

Brief Introduction

CloneTools package is comprised of several tools:

  1. Control clone picker;
  2. FASTA generator;
  3. Conserved region finder;
  4. Sequence filter;
  5. Clone plate reorder;
  6. Synthetic fingerprint generator.

(1) Control Clone Picker

A tool for selecting control clones for fingerprint classifications. In addition to sample clones, the microarrays in hybridization experiments contain a number of control clones with known sequences and hybridization properties, which are used to normalize the experimental results. Control clones for hybridization experiments need to be selected with great care to maximize the quality of information obtained in the experiments. (In the past, the selection of control clones for our experiments was done by hand.)

The program is given a collection of candidate control clones and a set of oligonucleotide probes chosen for hybridization experiments. Based on this information, from among the candidate clones, we want to select a specified number of control clones in such a way that each probe will hybridize with roughly half of them. This leads naturally to a combinatorial optimization problem that we call Balanced Covering. This tool is implemented based on an algorithm using linear programming and randomized rounding.

(2) FASTA Generator

This tool transforms RDP sequence files into FASTA sequence files.

(3) Conserved Region Finder

This tool allows the percentage of conserved bases at each position in a sequence alignment to be determined.

(4) Sequence Filter

This tool allows multiple sequences files to be manipulated in several ways: filters out repeated sequences, filters out sequences based on size, and also filters out sequences with any combination of ambiguous bases.

(5) Clone Plate Reorder

This tool facilitates practical aspects of organizing/tracking of clones for OFRG experiments.

(6) Synthetic Fingerprint Generator

This tool produces theoretical fingerprints, given a collection of nucleotide sequences and a set of oligonucleotide probes.


Algorithmic approaches to selecting control clones in DNA array hybridization experiments
Qi Fu, Elizabeth Bent, James Borneman, Marek Chrobak, Neal E Young J Bioinform Comput Biol. 2007 5(4):937-961


To run CloneTools, make sure that all files extracted from this zip file are in the same folder, and then run CloneTools.exe. The supported platform are Windows 2000/NT/XP.

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Copyright @ by Oligonucleotide Fingerprinting of Ribosomal RNA Genes(OFRG) Group (zliu@cs.ucr.edu, qfu@cs.ucr.edu), 2002

Last Modified on 04/25/2013