Abstract
As genome sequence data and gene prediction improve, probes developed for a given microarray experiment should be continuously re-evaluated for their specificity for given genes. ProbeLynx (www.pathogenomics.ca/probelynx) is a new web servicewhichusescurrentgenomicsequenceinformation to re-examine microarray probe specificity and provide annotation updates relevant to determining which gene(s) and transcript(s) are associated with a given probe. Probe sequences (either oligonucleotide- or cDNA-based) are uploaded in FASTA format and the results returned as a tab-delimited flat file for insertion into a spreadsheet application or database management system for further analysis. ProbeLynx has been initially developed to focus on arrays derived from human, mouse, chicken and bovine genomes, but may be expanded to handle other genomic datasets. ProbeLynx offers microarray users the important ability to continuously assess the potential of a probe to cross-hybridize to paralogous genes and the suitability of a given probe to investigate a transcript of interest. By also including the latest gene function annotation information in the output, ProbeLynx provides the critical first step in updating microarray data annotation.
| Language | English |
|---|---|
| Journal | Nucleic acids research |
| Volume | 32 |
| Issue number | WEB SERVER ISS. |
| DOIs | |
| Publication status | Published - 1 Jul 2004 |
ASJC Scopus subject areas
- Genetics
Cite this
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ProbeLynx : A tool for updating the association of microarray probes to genes. / Roche, Fiona M.; Hokamp, Karsten; Acab, Michael; Babiuk, Lorne A.; Hancock, Robert; Brinkman, Fiona S.L.
In: Nucleic acids research, Vol. 32, No. WEB SERVER ISS., 01.07.2004.Research output: Contribution to journal › Article
TY - JOUR
T1 - ProbeLynx
T2 - Nucleic Acids Research
AU - Roche, Fiona M.
AU - Hokamp, Karsten
AU - Acab, Michael
AU - Babiuk, Lorne A.
AU - Hancock, Robert
AU - Brinkman, Fiona S.L.
PY - 2004/7/1
Y1 - 2004/7/1
N2 - As genome sequence data and gene prediction improve, probes developed for a given microarray experiment should be continuously re-evaluated for their specificity for given genes. ProbeLynx (www.pathogenomics.ca/probelynx) is a new web servicewhichusescurrentgenomicsequenceinformation to re-examine microarray probe specificity and provide annotation updates relevant to determining which gene(s) and transcript(s) are associated with a given probe. Probe sequences (either oligonucleotide- or cDNA-based) are uploaded in FASTA format and the results returned as a tab-delimited flat file for insertion into a spreadsheet application or database management system for further analysis. ProbeLynx has been initially developed to focus on arrays derived from human, mouse, chicken and bovine genomes, but may be expanded to handle other genomic datasets. ProbeLynx offers microarray users the important ability to continuously assess the potential of a probe to cross-hybridize to paralogous genes and the suitability of a given probe to investigate a transcript of interest. By also including the latest gene function annotation information in the output, ProbeLynx provides the critical first step in updating microarray data annotation.
AB - As genome sequence data and gene prediction improve, probes developed for a given microarray experiment should be continuously re-evaluated for their specificity for given genes. ProbeLynx (www.pathogenomics.ca/probelynx) is a new web servicewhichusescurrentgenomicsequenceinformation to re-examine microarray probe specificity and provide annotation updates relevant to determining which gene(s) and transcript(s) are associated with a given probe. Probe sequences (either oligonucleotide- or cDNA-based) are uploaded in FASTA format and the results returned as a tab-delimited flat file for insertion into a spreadsheet application or database management system for further analysis. ProbeLynx has been initially developed to focus on arrays derived from human, mouse, chicken and bovine genomes, but may be expanded to handle other genomic datasets. ProbeLynx offers microarray users the important ability to continuously assess the potential of a probe to cross-hybridize to paralogous genes and the suitability of a given probe to investigate a transcript of interest. By also including the latest gene function annotation information in the output, ProbeLynx provides the critical first step in updating microarray data annotation.
UR - http://www.scopus.com/inward/record.url?scp=3242882897&partnerID=8YFLogxK
U2 - 10.1093/nar/gkh452
DO - 10.1093/nar/gkh452
M3 - Article
VL - 32
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - WEB SERVER ISS.
ER -