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Proceedings Paper

Designing oligo libraries taking alternative splicing into account
Author(s): Avi Shoshan; Vladimir Grebinskiy; Avner Magen; Ariel Scolnicov; Eyal Fink; David Lehavi; Alon Wasserman
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Paper Abstract

We have designed sequences for DNA microarrays and oligo libraries, taking alternative splicing into account. Alternative splicing is a common phenomenon, occurring in more than 25% of the human genes. In many cases, different splice variants have different functions, are expressed in different tissues or may indicate different stages of disease. When designing sequences for DNA microarrays or oligo libraries, it is very important to take into account the sequence information of all the mRNA transcripts. Therefore, when a gene has more than one transcript (as a result of alternative splicing, alternative promoter sites or alternative poly-adenylation sites), it is very important to take all of them into account in the design. We have used the LEADS transcriptome prediction system to cluster and assemble the human sequences in GenBank and design optimal oligonucleotides for all the human genes with a known mRNA sequence based on the LEADS predictions.

Paper Details

Date Published: 4 June 2001
PDF: 10 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427976
Show Author Affiliations
Avi Shoshan, Compugen Inc. (United States)
Vladimir Grebinskiy, Compugen Inc. (United States)
Avner Magen, Compugen Ltd. (Israel)
Ariel Scolnicov, Compugen Ltd. (Israel)
Eyal Fink, Compugen Ltd. (Israel)
David Lehavi, Compugen Ltd. (Israel)
Alon Wasserman, Compugen Inc. (United States)


Published in SPIE Proceedings Vol. 4266:
Microarrays: Optical Technologies and Informatics
Michael L. Bittner; Yidong Chen; Andreas N. Dorsel; Edward R. Dougherty, Editor(s)

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