Question

Favorite Splice Site Prediction/Evaluation Tools

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12.0 years ago

Alex Paciorkowski 3.5k

Does anyone have a favorite splice site prediction / evaluation tool? (This would be for evaluating variants in the human genome). I am familiar with the Human Splicing Finder, but am looking to try others. Open-source would be ideal, and if possible something that can be scripted into a workflow. Thanks.

splicing prediction • 19k views

ADD COMMENT • link updated 17 months ago by abhilashdasari.10 ▴ 30 • written 12.0 years ago by Alex Paciorkowski 3.5k

score 5 · Answer 1 · 2012-12-04

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12.0 years ago

Malachi Griffith 20k

A review of some potentially relevant tools, databases, algorithms, etc. can be found in Table 1.2 on page 52-53 of this thesis.

Also this post is highly relevant: Alternative splicing detection

ADD COMMENT • link 10.7 years ago by Malachi Griffith 20k

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Thesis link is not working

ADD REPLY • link 17 months ago by abhilashdasari.10 ▴ 30

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I really appreciate your sharing this -- thank you.

ADD REPLY • link 12.0 years ago by Alex Paciorkowski 3.5k

score 3 · Answer 2 · 2012-11-30

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12.0 years ago

swbarnes2 14k

This is the one I've used for a while, but its quite old:

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

Can't say I have any hard evidence of its accuracy, but it's easy to use. But I don't see how to incorporate it into a script

ADD COMMENT • link 12.0 years ago by swbarnes2 14k

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Thanks, I will definitely check this one out.

And I know -- it doesn't apparently bode well for one's research program to be asking about tools to evaluate intronic sequence...

ADD REPLY • link 12.0 years ago by Alex Paciorkowski 3.5k

score 3 · Answer 3 · 2013-07-01

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11.4 years ago

Venkatesh ▴ 30

Hi Alex, sorry if this reply is a bit late.

I have used Human Splicing Finder and GeneSplicer but I would recommend AspAlt (Alternative-splicing and Alternative Transcription) tool along with EuSplice.

Unfortunately, these are not open-source but the accuracy is impressive. They follow a scoring system for predicted cryptic splice sites and compare them with known splice junctions which I found useful. Again this is only my opinion, comments welcome!

HTH,

Venkatesh Patel

ADD COMMENT • link 11.4 years ago by Venkatesh ▴ 30

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Hi,

as Alex, I would like to score the impact of the mutations within splice sites and I've found this thread. Apparently it is not that evident to find the right tool to do that, so I write just in case someone has further ideas. Note that I am not interested -at that moment- in finding mutations leading to cryptic splice sites, but to score the importance of mutations in already known splice sites (according to variant effect predictor, for instance)

I already checked MaxEntScan and HumanSpliceFinder, but I do not find how to use them in a script (which I need!)

thanks, david

ADD REPLY • link 11.2 years ago by david.tamborero • 0

score 2 · Answer 4 · 2012-12-08

you can use maxent 5'ss or maxent 3'ss to evaluate them. a former post-doc in my lab (before i joined) developed it. the model gives you a splice site strength in units of bits, where higher values correspond to better splice sites. values below 0 tend to be annotation errors or have something weird going on. bits are additive, so you can subtract the variant's score from that of the consensus to determine the expected effect on splicing.

note that maxent does not accurately model u12 (ATAC) introns.

score 2 · Answer 5 · 2013-01-24

I just came over here to ask the same question with a focus on tools for plant RNA splice site prediction... Due to my best knowledge genesplicer (Pertea et al., 2001) is the latest available tool for A. thaliana. Another one is from the Brunak group: NetGene2 (Hebsgaard et al., 1996). I can't believe that there wasn't any progress in this field for the last five to ten years?