About ASviewer

Alternative splicing produces transcript variants by differential use of splice sites. Although comparing the structure of a given gene and splice variants is an essential step in understanding the function of the protein, the ultimate product of the transcript, it often is a nontrivial and tedious task if numerous combinations are possible. We present a novel viewer, ASviewer that visualizes the transcript structure and functional features of alternatively spliced variants. Two key ideas are clustering of overlapping exons and representing introns in a variable scale. Using the representative exons in the master coordinate facilitates the comparative structural analyses for genes with several splice variants. Variable intron scaling allows a seamless transition from the genome browser to the transcript or protein viewers. Thus, the detailed gene structure as well as known functional features in the genomic, mRNA, and protein sequences can be readily indicated in a single user interface. Current java implementation supports the four well-known gene predictions (RefSeq, Ensembl, AceView, and ECgene), and users may upload sequences, features, and annotations in various formats.

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