Abstract
In eukaryotes, different combinations of exons lead to multiple transcripts with various functions in protein level, in a process called alternative splicing (AS). Unfolding the complexity of functional genomics through genome-wide profiling of AS and determining the altered ultimate products provide new insights for better understanding of many biological processes, disease progress as well as drug development programs to target harmful splicing variants. The current available tools of alternative splicing work with raw data and include heavy computation. In particular, there is a shortcoming in tools to discover AS events directly from transcripts. Here, we developed a Windows-based user-friendly tool for identifying AS events from transcripts without the need to any advanced computer skill or database download. Meanwhile, due to online working mode, our application employs the updated SpliceGraphs without the need to any resource updating. First, SpliceGraph forms based on the frequency of active splice sites in pre-mRNA. Then, the presented approach compares query transcript exons to SpliceGraph exons. The tool provides the possibility of statistical analysis of AS events as well as AS visualization compared to SpliceGraph. The developed application works for transcript sets in human and model organisms.
Highlights
Transcripts are products of pre-mRNA splicing processes
Transcripts are the important output of many high throughput transcriptome analysis tools which are widely used in RNA-seq data analysis[13]
In addition to the splice sites support, we used features such as the length of exons and prioritized multiple exons over a continuous exon with the identical start and end coordinates to improve the SpliceGraph structure, get a better definition of differences between transcripts variants, and recognize all possible exons. Use of this software is as simple as Vials tool which works with the gene names, but we have provided the possibility to enter a set of transcripts in a using process, and we believe it as an advantage for our software
Summary
Transcripts are products of pre-mRNA splicing processes. Novel transcripts discover each day[1,2] and add to public databases. The second and third types of alternative splicing are related to both the 3′ and 5′ ends of exons(A5′ss & A3′ss). These types of AS events occur when there are more than one splice site at one end of an exon. The fourth type is introns retaining (RI) where introns remain in transcript This is the rarest known type in both vertebrates and invertebrates (less than 5 percent of AS events). There is another type of splicing type related to the latter type which includes a partial retention of an intron. Many of the AS finding tools do not have the sufficiency of finding AS events straightly from specified transcripts
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