Designing oligo libraries taking alternative splicing into account

Avi Shoshan; Vladimir Grebinskiy; Avner Magen; Ariel Scolnicov; Eyal Fink; David Lehavi; Alon Wasserman

doi:10.1117/12.427976

4 June 2001 Designing oligo libraries taking alternative splicing into account

Avi Shoshan, Vladimir Grebinskiy, Avner Magen, Ariel Scolnicov, Eyal Fink, David Lehavi, Alon Wasserman

Proceedings Volume 4266, Microarrays: Optical Technologies and Informatics; (2001) https://doi.org/10.1117/12.427976
Event: BiOS 2001 The International Symposium on Biomedical Optics, 2001, San Jose, CA, United States

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.

Citation Download Citation

Avi Shoshan, Vladimir Grebinskiy, Avner Magen, Ariel Scolnicov, Eyal Fink, David Lehavi, and Alon Wasserman "Designing oligo libraries taking alternative splicing into account", Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); https://doi.org/10.1117/12.427976

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