Selecting Probes for DNA Arrays")?>
One problem arising frequently in the design of DNA chips is the selection of target
specific probes. Given a set of genomic sequences, the task is to find at least one
short subsequence for each of the target sequences in this set. That subsequence will
then be attached to the chip, and must be chosen such that it will not hybridize to any
but the intended target. The problem is related to primer design for PCR experiments,
where minimizing cross-hybridization errors is an important issue as well, even though
certain different constraints apply.
The problem is complicated if sequences are to be chosen such that they will properly
hybridize to a group (e.g. a complete family of organisms), but not to any organism from
a different group.
We present an efficient algorithm for the array probe selection problem. Melting
temperatures and free energy for each possible sequence-probe interaction are calculated
using an extended nearest neighbor model, allowing for mismatches. Model parameters can
easily be adapted when new parameters are published, and alternatively parameters for DNA
or RNA assays can be used. Hairpins, bulge loops and other secondary structure can also
be considered.
The algorithm can easily be modified to select family-specific probes.
Data:")?>
The following files show sample data for the HIV-1 subtypes as referred to in the published paper.
HIV1.FASTA Fasta format file containing the HIV1 subtypes used.
HIV1.PRB Oligo probes selected by the algorithm
Contact:")?>Lars Kaderali
kaderali@zpr.uni-koeln.de
Download")?>
GCB 2000 Poster (PS GZIP)
GCB 2000 Poster Abstract (PS)
Diploma Thesis (Fulltext) PS GZIP
Paper (PDF), published in Bioinformatics 2002; 18(10):1340-9, (c) Oxford University Press.
ISMB 2001 Poster (EPS)