A weight array method for splicing signal analysis - PubMed (original) (raw)
A weight array method for splicing signal analysis
M Q Zhang et al. Comput Appl Biosci. 1993 Oct.
Abstract
A new method of sequence analysis, using a weight array method (WAM), which generalizes the traditional Staden weight matrix method (WMM), is proposed. With the help of a statistical mechanical model, the discriminant function is identified with the energy function describing macromolecular interactions. The method is applied to the study of 5'-splice signals in Schizosaccharomyces pombe pre-mRNA sequences. The results show that there may exist weak pairwise correlations within the signals and that our method can help to better discriminate these signals. Experiments are proposed to test the predictions of the theory.
Similar articles
- Architectural features of pre-mRNA introns in the fission yeast Schizosaccharomyces pombe.
Prabhala G, Rosenberg GH, Käufer NF. Prabhala G, et al. Yeast. 1992 Mar;8(3):171-82. doi: 10.1002/yea.320080303. Yeast. 1992. PMID: 1574925 - Pre-mRNA splicing in Schizosaccharomyces pombe: regulatory role of a kinase conserved from fission yeast to mammals.
Kuhn AN, Käufer NF. Kuhn AN, et al. Curr Genet. 2003 Feb;42(5):241-51. doi: 10.1007/s00294-002-0355-2. Epub 2002 Dec 13. Curr Genet. 2003. PMID: 12589463 Review. - Molecular genetic analysis of U2AF59 in Schizosaccharomyces pombe: differential sensitivity of introns to mutational inactivation.
Romfo CM, Lakhe-Reddy S, Wise JA. Romfo CM, et al. RNA. 1999 Jan;5(1):49-65. doi: 10.1017/s1355838299981323. RNA. 1999. PMID: 9917066 Free PMC article. - prp4 from Schizosaccharomyces pombe, a mutant deficient in pre-mRNA splicing isolated using genes containing artificial introns.
Rosenberg GH, Alahari SK, Käufer NF. Rosenberg GH, et al. Mol Gen Genet. 1991 Apr;226(1-2):305-9. doi: 10.1007/BF00273617. Mol Gen Genet. 1991. PMID: 2034223 - Structure and function of the Pre-mRNA splicing machine.
Sperling J, Azubel M, Sperling R. Sperling J, et al. Structure. 2008 Nov 12;16(11):1605-15. doi: 10.1016/j.str.2008.08.011. Structure. 2008. PMID: 19000813 Review.
Cited by
- Motif models proposing independent and interdependent impacts of nucleotides are related to high and low affinity transcription factor binding sites in Arabidopsis.
Tsukanov AV, Mironova VV, Levitsky VG. Tsukanov AV, et al. Front Plant Sci. 2022 Jul 28;13:938545. doi: 10.3389/fpls.2022.938545. eCollection 2022. Front Plant Sci. 2022. PMID: 35968123 Free PMC article. - Disentangling transcription factor binding site complexity.
Eggeling R. Eggeling R. Nucleic Acids Res. 2018 Nov 16;46(20):e121. doi: 10.1093/nar/gky683. Nucleic Acids Res. 2018. PMID: 30085218 Free PMC article. - Identification of donor splice sites using support vector machine: a computational approach based on positional, compositional and dependency features.
Meher PK, Sahu TK, Rao AR, Wahi SD. Meher PK, et al. Algorithms Mol Biol. 2016 Jun 1;11:16. doi: 10.1186/s13015-016-0078-4. eCollection 2016. Algorithms Mol Biol. 2016. PMID: 27252772 Free PMC article. - Prediction of donor splice sites using random forest with a new sequence encoding approach.
Meher PK, Sahu TK, Rao AR. Meher PK, et al. BioData Min. 2016 Jan 22;9:4. doi: 10.1186/s13040-016-0086-4. eCollection 2016. BioData Min. 2016. PMID: 26807151 Free PMC article. - Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data.
Eggeling R, Roos T, Myllymäki P, Grosse I. Eggeling R, et al. BMC Bioinformatics. 2015 Nov 9;16:375. doi: 10.1186/s12859-015-0797-4. BMC Bioinformatics. 2015. PMID: 26552868 Free PMC article.