TRANSCRIPTOME 2002: From Functional Genomics to Systems Biology
March 10-13, 2002
Seattle, Washington, USA


Paracel TranscriptAssembler:  Identification of Splice Variants for Gene Discovery and Gene Expression Profiling

Cecilie Boysen, Stephanie S. Pao, Jun Qian, Charles P. Smith, Lingyan Zhu, and Joseph A. Borkowski, Paracel, Inc., Pasadena, CA

Alternative splice forms play a major role in modifying physiological processes. Although the human genome may have fewer genes than originally thought, many of these give rise to multiple different transcripts. These alternative splice forms can be specific to certain environments, tissues, and drug treatments. A thorough investigation of genes involved in biological functions requires analysis of the corresponding splice variants. Many splice variants can be identified by comparing EST and mRNA sequences originating from the same gene. This can be done even when the genomic sequence is not known, which makes it widely applicable to plant and animal studies. Paracel TranscriptAssembler has been used to recognize splice variants in the transcriptome of various species. Capable of clustering and assembling millions of ESTs and mRNAs, Paracel Transcript-Assembler addresses technical and biological problems in this process, such as chimeric sequences, low quality sequences, repeats, and splice variants. Following the resolution of splice variants into separate contigs, Paracel TranscriptAssembler performs an alignment of the resulting consensus sequences and displays the relationship between splice forms. Specific gene segments are generated for each variant and can be used directly in splice variant specific oligo design for gene expression assays.

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