Nucleic Acids Research, 2003, Vol. 31, No. 1 82-86
© 2003 Oxford University Press
NetAffx: Affymetrix probesets and annotations
Department of Bioinformatics, Affymetrix, Inc, 6550 Vallejo Street, Suite 100, Emeryville, CA 94608, USA
*To whom correspondence should be addressed. Email: guoying_liu{at}affymetrix.com
ABSTRACT
NetAffx (http://www.affymetrix.com) details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii) sequence annotations extracted from public databases; and (iii) protein sequence-level annotations derived from public domain programs, as well as libraries of hidden Markov models (HMMs) developed at Affymetrix. For each probeset, NetAffx lists the probe sequences, and the consensus sequence interrogated by the probes; for the larger chip sets, interactive maps display this sequence data in genomic context. Sequence annotations include Gene Ontology (GO) terms and depiction of GO graph relationships; predicted protein domains and motifs; orthologous sequences; links to relevant pathways; and links to public databases including UniGene, LocusLink, SWISS-PROT and OMIM.
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|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
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|
|
|
|
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|
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|
|
 |
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|
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|
|
|
|
 |
|
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|
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|
|
|
|
|
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|
|