Computational methods for alternative splicing prediction

Briefings in Functional Genomics and Proteomics

Volumn 5, Issue 1, 2006, Pages 46-51

  Bonizzoni, Paola ^a   Rizzi, Raffaella ^a   Pesole, Graziano ^b  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b UNIVERSITY OF BARI   (Italy)

Author keywords

Algorithm; Alternative splicing; Comparative genomics; Gene regulation; Software

Indexed keywords

COMPLEMENTARY DNA; GENOMIC DNA; MESSENGER RNA; PROTEOME;

ACCURACY; ALTERNATIVE RNA SPLICING; BIOINFORMATICS; COMPUTER MEMORY; COMPUTER PREDICTION; COMPUTER PROGRAM; EXPRESSED SEQUENCE TAG; GENE DELETION; GENE INSERTION; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC TRANSCRIPTION; HUMAN; INTRON; PARALOGY; RELIABILITY; REVIEW; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; ANIMAL; GENOME; PREDICTION AND FORECASTING; SEQUENCE ANALYSIS;

MAMMALIA;

ALGORITHMS; ALTERNATIVE SPLICING; ANIMALS; EXPRESSED SEQUENCE TAGS; GENOME; GENOME, HUMAN; HUMANS; PREDICTIVE VALUE OF TESTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 33745945162     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/ell011     Document Type: Review

References (20)

1. Graveley BR. Alternative splicing: Increasing diversity in the proteomic world. Trends Genet 2001;17:100-7.
2. Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res 2002;12:656-64.
3. Wheelan SJ, Church DM, Ostell JM. Spidey: A tool for mRNA-to-genomic alignments. Genome Res 2001;11: 1952-7.
4. Florea L, Hartzell G, Zhang Z, et al. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998;8:967-74.
5. Brett D, Hanke J, Lehmann G, et al. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett 2000;474:83-6.
6. Heber S, Alekseyev M, Sze SH, et al. Splicing graphs and EST assembly problem. Bioinformatics 2002;18(Suppl 1): S181-8.
7. Burset M, Seledtsov IA, Solovyev VV. Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res 2000;28:4364-75.
8. Mott R. EST_GENOME: A program to align spliced DNA sequences to unspliced genomic DNA. Comput Appl Biosci 1997;13:477-8.
9. Usuka J, Zhu W, Brendel V. Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics 2000;16:203-11.
10. Lee BT, Tan TW, Ranganathan S. MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences. Nucleic Acids Res 2003;31:3533-6.
11. Ogasawara J, Morishita S. Fast and sensitive algorithm for aligning ESTs to human genome. Proc IEEE Comput Soc Bioinform Conf 2002;1:43-53.
12. Wu TD, Watanabe CK. GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005;21:1859-75.
13. Bonizzoni P, Rizzi R, Pesole G. ASPIC: A novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. BMC Bioinformatics 2005;6:244.
14. Setubal J, Meidanis J. Introduction to Computational Molecular Biology. Boston MA: PWS Publishing Company, 1997.
15. Kim N, Shin S, Lee S. ECgene: Genome-based EST clustering and gene modeling for alternative splicing. Genome Res 2005;15:566-76.
16. Grasso C, Modrek B, Xing Y, Lee C. Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs. Pac Symp Biocomput 2004;1:29-41.
17. Xing Y, Resch A, Lee C. The multiassembly problem: Reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res 2004;14:426-41.
18. Shapiro MB, Senapathy P. RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression. Nucleic Acids Res 1987;15:7155-74.
19. Eyras E, Caccamo M, Curwen V, et al. ESTGenes: Alternative splicing from ESTs in Ensembl. Genome Res 2004;14:976-87.
20. Leipzig J, Pevzner P, Heber S. The alternative splicing gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res 2004;32:3977-83.