Can Software Predict RNA Splicing Sites?

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Discussion Overview

The discussion revolves around the prediction of RNA splicing sites using software tools. Participants explore various software options and express differing views on the nature of splicing and the role of introns and exons in this process.

Discussion Character

  • Exploratory, Technical explanation, Debate/contested

Main Points Raised

  • One participant inquires about software used for predicting RNA splicing sites.
  • Another participant mentions a specific software program from the Institute for Genomic Research (TIGR) as a freely available option.
  • A third participant provides a link to a comprehensive collection of bioinformatics tools relevant to gene identification.
  • One participant expresses a desire for software that does not separate introns and exons, suggesting a belief that splicing occurs within introns.
  • Another participant counters that knowing the locations of introns and exons can help deduce splice sites and notes that existing software may struggle with accurate predictions, particularly for the first splice site.
  • This participant also suggests that if alternative splicing is suspected, molecular biology experiments may be necessary.

Areas of Agreement / Disagreement

Participants exhibit differing views on the necessity of separating introns and exons for predicting splice sites, indicating a lack of consensus on the best approach to RNA splicing prediction.

Contextual Notes

Some assumptions about the nature of splicing and the capabilities of software tools remain unaddressed, and there is uncertainty regarding the accuracy of predictions made by the mentioned software.

karthik3k
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RNA Splicing Software ?

What is the Softwares used to predict RNA splicing sites ?
 
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I don't know which ones are regarded the best, but http://www.tigr.org/tdb/GeneSplicer/gene_spl.html" is a software program freely available through the Institute for Genomic Research (TIGR).
 
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Hey thanks :)

But, i don't want anything which sequesters introns and exons.

Coz i suspect that splicing takes place inside INTRON.
So software has 2 identify only the site of action and not separating introns and exons !
 
? but if you know where the introns and exons are, you can automatically deduce the splice site.. and these software programs are not perfect in predicting splicing, especially the first one is difficult to get correct I believe.

If you suspect alternative splicing is taking place, I'd do some molecular biology experiments..
 

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