chipD: a web tool to design oligonucleotide probes for high-density tiling arrays.
chipD is a web server that facilitates design of DNA oligonucleotide probes for high-density tiling arrays, which can be used in a number of genomic applications such as ChIP-chip or gene-expression profiling. The server implements a probe selection algorithm that takes as an input, in addition to the target sequences, a set of parameters that allow probe design to be tailored to specific applications, protocols or the array manufacturer's requirements. The algorithm optimizes probes to meet three objectives: (i) probes should be specific; (ii) probes should have similar thermodynamic properties; and (iii) the target sequence coverage should be homogeneous and avoid significant gaps. The output provides in a text format, the list of probe sequences with their genomic locations, targeted strands and hybridization characteristics. chipD has been used successfully to design tiling arrays for bacteria and yeast. chipD is available at http://chipd.uwbacter.org/.
Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA. ydufour@wisc.edu
Yann S
YS
Dufour
Gary E
GE
Wesenberg
Andrew J
AJ
Tritt
Jeremy D
JD
Glasner
Nicole T
NT
Perna
Julie C
JC
Mitchell
Timothy J
TJ
Donohue
D000465:Algorithms; D020869:Gene Expression Profiling; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes / Q000737:chemistry*; D012242:Rhodobacter sphaeroides / Q000235:genetics; D012984:Software; D014584:User-Computer Interface
D015345:Oligonucleotide Probes