title: A statistical approach for 5' splice site prediction using short sequence motifs and without encoding sequence data.
abstract: BACKGROUND
  Most of the approaches for splice site prediction are based on machine learning techniques. Though, these approaches provide high prediction accuracy, the window lengths used are longer in size. Hence, these approaches may not be suitable to predict the novel splice variants using the short sequence reads generated from next generation sequencing technologies. Further, machine learning techniques require numerically encoded data and produce different accuracy with different encoding procedures. Therefore, splice site prediction with short sequence motifs and without encoding sequence data became a motivation for the present study.
  
  
  RESULTS
  An approach for finding association among nucleotide bases in the splice site motifs is developed and used further to determine the appropriate window size. Besides, an approach for prediction of donor splice sites using sum of absolute error criterion has also been proposed. The proposed approach has been compared with commonly used approaches i.e., Maximum Entropy Modeling (MEM), Maximal Dependency Decomposition (MDD), Weighted Matrix Method (WMM) and Markov Model of first order (MM1) and was found to perform equally with MEM and MDD and better than WMM and MM1 in terms of prediction accuracy.
  
  
  CONCLUSIONS
  The proposed prediction approach can be used in the prediction of donor splice sites with higher accuracy using short sequence motifs and hence can be used as a complementary method to the existing approaches. Based on the proposed methodology, a web server was also developed for easy prediction of donor splice sites by users and is available at http://cabgrid.res.in:8080/sspred .
authors.affiliation: Division of Statistical Genetics, Indian Agricultural Statistics Research Institute, New Delhi, 110012, India. meherprabin@yahoo.com.
authors.forename: Prabina Kumar
authors.initials: PK
authors.lastname: Meher
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, 110012, India. tanmayabioinfo@gmail.com.
authors.forename: Tanmaya Kumar
authors.initials: TK
authors.lastname: Sahu
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, 110012, India. rao.cshl.work@gmail.com.
authors.forename: Atmakuri Ramakrishna
authors.initials: AR
authors.lastname: Rao
authors.affiliation: Division of Statistical Genetics, Indian Agricultural Statistics Research Institute, New Delhi, 110012, India. sdwahi@iasri.res.in.
authors.forename: Sant Dass
authors.initials: SD
authors.lastname: Wahi
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D015233:Models, Statistical; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics*; D012372:ROC Curve; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D022821:RNA Splice Sites