Actually i have to find out the type of Alternative splicing eg. exon skipping, from the transcriptome data. I am not familiar with R packages and linux system. Earlier i was using ASFinder and unfortunately the web service was stopped. Hence i am looking for similar web based tools. Can anyone Pls help me ?Thanks in advance
I would recommend the genome browser (link bellow). You can search by organism and by gene and you will have a graphic view of each exon in each alternative transcript. In addition you can use the tool "BLAT" to copy your sequence of interest and view it either as "browser" (the graphic view) or "details" were the exons and introns are highlighted. In the browser view you will see "your sequence" on top and it will be really easy to determine exon skipping or exon inclusion. For mutually exclusive exons both sequences of the alternatively transcribed mRNAs have to be in the database or you have to know them. This page has been up for many years and is constantly updated and improved. Use the "help" if needed , but in general try to click on everything for more info and features.
http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=453567845_v6mswwyrAOwWQJFa50wsaZgSWa3x
Thanks Soledad. I think i have to mention here that i am working on a Plant transcriptome -Banana. Yes i came across the link previously but that is only for Animals. One more think is have to see all types of splicing(intron retaining, exon skipping, donor and acceptor site etc) in large seq data. Hence some web tools having size restrictions no use for me.
Hi,
I'm not quite sure if you are asking for a tool to analyse open source/your own RNA seq data (compare it to known sequences/genome) or if you want a database for known splicing events. For the first you can use galaxy to prepare your data and in the end align with IGV for example. There are numerous ways of doing it and intron retention detection can be quite difficult. Again I have no experience with plant studies.
I hope this was of some help!
https://galaxyproject.org/
http://www.broadinstitute.org/igv/home
@Muthu, I understand your query. There's is no such resource available for plant genomes esp. for a recently assembled genome like Musa.
If you are interested in developing such a database for Banana transcriptome, please inbox me. We already have a database that does exactly what you have asked here but in animals. So do message me!
@ Venkatesh Thanks for your reply. I ll let you know if we plant to develop a database in future
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