Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
19
pubmed:dateCreated
2005-10-25
pubmed:abstractText
The oligonucleotide specificity for microarray hybridization can be predicted by its sequence identity to non-targets, continuous stretch to non-targets, and/or binding free energy to non-targets. Most currently available programs only use one or two of these criteria, which may choose 'false' specific oligonucleotides or miss 'true' optimal probes in a considerable proportion. We have developed a software tool, called CommOligo using new algorithms and all three criteria for selection of optimal oligonucleotide probes. A series of filters, including sequence identity, free energy, continuous stretch, GC content, self-annealing, distance to the 3'-untranslated region (3'-UTR) and melting temperature (T(m)), are used to check each possible oligonucleotide. A sequence identity is calculated based on gapped global alignments. A traversal algorithm is used to generate alignments for free energy calculation. The optimal T(m) interval is determined based on probe candidates that have passed all other filters. Final probes are picked using a combination of user-configurable piece-wise linear functions and an iterative process. The thresholds for identity, stretch and free energy filters are automatically determined from experimental data by an accessory software tool, CommOligo_PE (CommOligo Parameter Estimator). The program was used to design probes for both whole-genome and highly homologous sequence data. CommOligo and CommOligo_PE are freely available to academic users upon request.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-10090733, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-10329189, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-10383469, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-10481021, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-10929718, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-11071945, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-11283592, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-11724738, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-11836214, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-11934750, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12034852, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12180093, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12620119, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12651953, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12724288, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12799432, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12824351, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12824409, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12824412, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-12831906, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-15088384, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-15240314, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-16000786, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-1711369, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-2231712, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-2479010, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-9381177, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-9415887, http://linkedlifedata.com/resource/pubmed/commentcorrection/16246912-9465037
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
1362-4962
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
33
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
6114-23
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2005
pubmed:articleTitle
Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation.
pubmed:affiliation
PerkinElmer Life and Analytical Sciences, 549 Albany Street, Boston, MA 02118, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S.