Alternative splicing is the major contributor for protein diversity. The splicing mechanism recognizes the boundaries between exons and introns. Alternative splicing can be a mechanism to generate more than one mRNA and protein from a single gene. Cancer associated splice variants have been reported for many genes involve misregulation of alternative splicing and errors in mRNA, meanwhile, alternative splicing can display a family of different protein in different tissues. Expressed sequence tags (ESTs) represent partial mRNA sequence and have provided the most comprehensive window into the transcriptome. NCBI dbEST, the biggest EST database in the world, has nearly 5.5 million human ESTs. AVATAR, a value added transcriptome data base, which was developed by aligning ESTs (expressed sequence tag) to genomic sequences directly, offers resources to analyze EST expressed in many tissues at each alternative splicing sites. In this research, each alternative splicing sites is tested if it is related with tumor or not by Fisher’s exact test. 51 tumor-specific alternative splicing sites are detected, and 11 of them are cancer related genes which are mentioned in NCBI LocusLink. Besides detecting tumor-specific alternative splicing sites, serial EST alignment, gene structure presentation and motif marker tools are developed and integrated.
