Abstract:
: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/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dufour YS,Wesenberg GE,Tritt AJ,Glasner JD,Perna NT,Mitchell JC,Donohue TJdoi
10.1093/nar/gkq517subject
Has Abstractpub_date
2010-07-01 00:00:00pages
W321-5issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkq517journal_volume
38pub_type
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