UFOHunter is a web-based utility for the design of optimal oligonucleotide
probes for DNA microarray, which employs the Markov Chain Analysis (MCA).
The oligonucleotide probes are designed based on the following considerations:
Minimum frequency in the target sequence pool. Frequencies of candidate probes are estimated
by MCA.
Appropriate melting temperature.
No secondary structure.
Heuristics: no more than 5 C/G in a row; no more than 6 A/T in a row
(Lockhart 1996); no stretch of contiguous complementary sequence (>15bp)
with 100% similarity for sequences with overall similarity between 75~80% (Kane 2000).
Since the complexity of our algorithm is O(n), the speed is 2-3 order
of magnitude faster than conducting homology search with Blast. More
efficient implementation of this algorithm, like integration of
frequencies estimation within database and rewriting the codes with C,
will further improve the speed.
You may start with your probe design with
UFOHunter. Currently, we support the design of probes for human and mouse expression array, as well as human genomic array.
Correlation
between frequency estimated by 13-order MCA and BLAST score.
The original data for MCA and BLAST comparison is available here.
Oligonucleotide probes for totally 14,038 mRNA sequences from NCBI RefSeq (released at 06/15/2001) have been designed by our program.
Last modified: 12-25-01.
Copyright(C) 2001 Kun Zhang. All rights reserved.