Question: (Closed) Alternative splicing prediction
0
gravatar for rajesh
3.2 years ago by
rajesh 60
India/Chandigarh/
rajesh 60 wrote:

Is there is no algorithm that can predict alternative splicing event in human genome. Thanks in advance...

rna-seq chip-seq sequence genome • 1.7k views
ADD COMMENTlink modified 24 months ago by RamRS25k • written 3.2 years ago by rajesh 60

Do you mean predict on the basis of gene sequence which of its exons are constitutively spliced vs which ones are alternatively spliced?

ADD REPLYlink written 3.2 years ago by Satyajeet Khare1.5k

yeah prediction on the basis of gene sequence.

ADD REPLYlink written 3.2 years ago by rajesh 60

I see some tools online such as ASSP, AVISPA, HSF. Have you tried any of these? Do they work for your kind of analysis?

ADD REPLYlink written 3.2 years ago by Satyajeet Khare1.5k

I want to develop my own. So how can i beat them..could you have any idea...

ADD REPLYlink written 3.2 years ago by rajesh 60

Do you mean what they are lacking? I don't know for sure. For any tool, you can either increase the efficiency or add more features to it. You can collaborate with a biologist and compare all these tools for their efficiency if no one has done it so far. May be that will give a clue.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Satyajeet Khare1.5k

Hello rajesh !

We believe that this post does not fit the main topic of this site.

OP does not respond to posts after asking questions. Question closed until OP responds.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 24 months ago by RamRS25k
0
gravatar for vakul.mohanty
3.2 years ago by
vakul.mohanty240
United States
vakul.mohanty240 wrote:

There are plenty of bioinformatic tools out there that predict alternative splicing events from RNAseq (or other data, I'm not sure). (http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4680). You look through the tools listed in the link to find a tool that suits your need.

ADD COMMENTlink written 3.2 years ago by vakul.mohanty240
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