splicing predicton for NGS data

[rudi283]

Hi,
I was wondering if you know any free tool for splicing prediction for NGS data? All tools I found required pasting sequence of the gene + sequence with mutation. I need to analyze several hundred genes and it'll take me forever trying to do it one by one for all the genes and all the mutations. Is there any way of doing it a bit quicker?
If you could suggest something would be really great as it's a bit daunting at the moment

[Bukowski]

Hi,
I was wondering if you know any free tool for splicing prediction for NGS data? All tools I found required pasting sequence of the gene + sequence with mutation. I need to analyze several hundred genes and it'll take me forever trying to do it one by one for all the genes and all the mutations. Is there any way of doing it a bit quicker?
If you could suggest something would be really great as it's a bit daunting at the moment

Feed your list of variants into something like Variant Effect Predictor:

http://www.ensembl.org/info/docs/variation/vep/index.html

It will predict consequences such as splice acceptor and splice donor variants and other variants potential affecting splicing sites.

That is assuming your looking for disruption of splicing sites, and not trying to predict transcripts from the data.

[rudi283]

Thank you very much!
I'll definitely have a go, when the ensembl will be back on on Monday