RNA Splicing and Alternative Splicing Predictive Software and Websites

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R Bishop
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RNA Splicing and Alternative Splicing Predictive Software and Websites

Thought it might be nice to have a list of RNA Splicing Tools Ive found and tried online.  If you are familiar with any of these please give it a review!
 
1. Alternative Splicing Database Project   - www.ebi.ac.uk/asd/
The Alternate Transcript Diversity Project (ATD) Project aims to understand the mechanisms that are responsible for the formation of transcript isoforms on a genome-wide scale by creating a value-added database of full-length alternate transcripts from human and mouse.
2. ASmodeler : Gene Modeling of Alternative Splicing Events  genome.ewha.ac.kr/ECgene/ASmodeler/
 
ASmodeler is a versatile program that can be used for various purposes. We will give a brief explanation for three example applications below.
(1) Genome-based sequence clustering and gene modeling for alternative splicing. This is the original purpose of the program, integration of clustering and assembly processes based on genomic alignments. Even if a gene is not alternatively spliced, ASmodeler can still be used as a sequence clustering utility based on genomic alignments.
(2) Transcript assembly for UniGene clusters. Even though NCBI¡¯s UniGene switched to the genome-based method for human, mouse, and rat genomes, UniGene itself does not provide any consensus sequences or splice variant analysis. ASmodeler can be utilized as a gene-modeling program for UniGene clusters, which gives consensus sequences with alternative splicing events taken into consideration. Furthermore, web-implementation enables the user to add private sequences to find any additional variants.
(3) Comparative gene modeling of alternative splicing. Many alternative splicing patterns are conserved between different species. Protein and/or mRNA sequences from other organisms may be supplied as an input to see if they produce any additional splice variants or the splice pattern is conserved between species. It is worth to verify new splice variants, if any, experimentally. This is particularly important for protein sequences since the resulting splice variations occur inside the coding