dont know

“All” might be difficult to achieve. “Online” options depend on the target species. For example, if you want to predict in mouse, you can use WebAUGUSTUS. In addition to the genomic locus you should provide extrinsic evidence from many splice isoforms (e.g. from RNASeq alignment). It is possible to sample alternative transcripts even without evidence but the false positive rate will be much higher. WebAUGUSTUS has a set of pretrained parameters for several species for this type of job. If you are dealing with a new species, you will need whole genome data for training AUGUSTUS. In any case, prediction of all possible splicing isoforms is not guaranteed.

You can use any genome browser to visualize the splicing isoforms, e.g. UCSC Genome Browser (maybe try https://github.com/Gaius-Augustus/MakeHub or if you are a Galaxy user try http://gonramp.wustl.edu/ ), the latter also allows you to set up JBrowse instances, which might be convenient for you.

Dear kathariana Hoff

Thanks for your answer. I forgot to mentioned that i am dealing with plant species. Anyway i understand that it is very hard to predict using online tools.

You can use WebAUGUSTUS for plants. There are a couple of paramete sets for plants.

Dear Katharina Hoff

Yes i am exploring it just after your previous comments. Thanks once again

http://wangcomputing.com/assp/

http://www.phenosystems.com/www/index.php/links-to-various-tools-and-information/splice-prediction-tools

http://www.fruitfly.org/seq_tools/splice.html

https://ccb.jhu.edu/software/genesplicer/

Thanks Dr. Avinash Marwal. I will check out the links