Abstract:
:Sequencing by hybridization (SBH) approaches to DNA sequencing face two conflicting constraints. First, in order to ensure that the target DNA binds reliably, the oligonucleotide probes that are attached to the chip array must be >15 bp in length. Secondly, the total number of possible 15 bp oligonucleotides is too large (>4(15)) to fit on a chip with current technology. To circumvent the conflict between these two opposing constraints, we present a novel gene-specific DNA chip design. Our design is based on the idea that not all conceivable oligonucleotides need to be placed on a chip--only those that capture sequence combinations occurring in nature. Our approach uses a training set of aligned sequences that code for the gene in question. We compute the minimum number of oligonucleotides (generally 15-30 bp in length) that need to be placed on a DNA chip to capture the variation implied by the training set using a graph search algorithm. We tested the approach in silico using cytochrome-b sequences. Results indicate that on average, 98% of the sequence of an unknown target can be determined using the approach.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Fedrigo O,Naylor Gdoi
10.1093/nar/gkh210keywords:
subject
Has Abstractpub_date
2004-02-18 00:00:00pages
1208-13issue
3eissn
0305-1048issn
1362-4962pii
32/3/1208journal_volume
32pub_type
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journal_title:Nucleic acids research
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