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Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region

BACKGROUND: Identifying reliable oligonucleotide sequences for use in microarray experiments is a complex process. Two key issues are the accuracy of the input sequences and the specificity of the oligonucleotide sequences. RESULTS: We provide a suite of Perl scripts that facilitates the search for...

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Detalles Bibliográficos
Autores principales: Chen, Hao, Sharp, Burt M
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2002
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC130177/
https://www.ncbi.nlm.nih.gov/pubmed/12366869
http://dx.doi.org/10.1186/1471-2105-3-27
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author Chen, Hao
Sharp, Burt M
author_facet Chen, Hao
Sharp, Burt M
author_sort Chen, Hao
collection PubMed
description BACKGROUND: Identifying reliable oligonucleotide sequences for use in microarray experiments is a complex process. Two key issues are the accuracy of the input sequences and the specificity of the oligonucleotide sequences. RESULTS: We provide a suite of Perl scripts that facilitates the search for gene-specific oligonucleotides for microarray experiments. Genes of interest are first identified in the form of UniGene clusters. The sequences of these clusters were extracted and assembled into contigs to increase their accuracy. The 3' untranslated region (3'UTR) of the contig was parsed. Then, multiple 50mer oligonucleotide sequences with similar melting temperature were obtained from each 3'UTR. These sequences were analyzed for gene specificity. Five Cy3-labeled cDNAs were used to empirically verify the specificity of a set of 1814 50mers. CONCLUSION: Oliz can be used to select oligonucleotide sequences for microarrays. Oliz is freely available for academic users at http://www.utmem.edu/pharmacology/otherlinks/oliz.html
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spelling pubmed-1301772002-11-01 Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region Chen, Hao Sharp, Burt M BMC Bioinformatics Methodology article BACKGROUND: Identifying reliable oligonucleotide sequences for use in microarray experiments is a complex process. Two key issues are the accuracy of the input sequences and the specificity of the oligonucleotide sequences. RESULTS: We provide a suite of Perl scripts that facilitates the search for gene-specific oligonucleotides for microarray experiments. Genes of interest are first identified in the form of UniGene clusters. The sequences of these clusters were extracted and assembled into contigs to increase their accuracy. The 3' untranslated region (3'UTR) of the contig was parsed. Then, multiple 50mer oligonucleotide sequences with similar melting temperature were obtained from each 3'UTR. These sequences were analyzed for gene specificity. Five Cy3-labeled cDNAs were used to empirically verify the specificity of a set of 1814 50mers. CONCLUSION: Oliz can be used to select oligonucleotide sequences for microarrays. Oliz is freely available for academic users at http://www.utmem.edu/pharmacology/otherlinks/oliz.html BioMed Central 2002-10-06 /pmc/articles/PMC130177/ /pubmed/12366869 http://dx.doi.org/10.1186/1471-2105-3-27 Text en Copyright ©2002 Chen and Sharp; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
spellingShingle Methodology article
Chen, Hao
Sharp, Burt M
Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
title Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
title_full Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
title_fullStr Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
title_full_unstemmed Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
title_short Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
title_sort oliz, a suite of perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region
topic Methodology article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC130177/
https://www.ncbi.nlm.nih.gov/pubmed/12366869
http://dx.doi.org/10.1186/1471-2105-3-27
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