Asfinder: A tool for genome-wide identification of alternatively splicing transcripts from EST-derived sequences

International Journal of Bioinformatics Research and Applications

Volumn 9, Issue 3, 2013, Pages 221-226

  Min, Xiang Jia ^a  

^a YOUNGSTOWN STATE UNIVERSITY   (United States)

Author keywords

Alternative Splicing; Cdna; Genome; Mapping; Tool

Indexed keywords

EID: 84877279721     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2013.053603     Document Type: Article

References (11)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) 'Basic local alignment search tool', J. Mol. Biol., Vol. 215, pp.403-410.
2. Edgar, R.C. (2004) 'MUSCLE: multiple sequence alignment with high accuracy and high throughput', Nucleic Acids Res., Vol. 32, pp.1792-1797.
3. Florea, L. (2006) 'Bioinformatics of alternative splicing and its regulation', Brief. Bioinform., Vol. 7, pp.55-69.
4. Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M. and Miller, W. (1998) 'A computer program for aligning a cDNA sequence with a genomic DNA sequence', Genome Res., Vol. 8, pp.967-974.
5. Foissac, S. and Sammeth, M. (2007) 'ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets', Nucleic Acids Res., Vol. 35 (Web Server issue), pp.297-299.
6. Garcia-Blanco, M.A., Baraniak, A.P. and Lasda, E.L. (2004) 'Alternative splicing in disease and therapy', Nature Biotech., Vol. 22, pp.535-546.
7. Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith Jr., R.K., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D., Salzberg, S.L. and White, O.I. (2003) 'Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies', Nucleic Acids Res., Vol. 31, pp.5654-5666.
8. Keren, H., Lev-Maor, G. and Ast, G. (2010) Alternative splicing and evolution: diversification, exon definition and function', Nature Rev. Genet., Vol. 11, pp.345-355.
9. Min, X.J., Butler, G., Storms, R. and Tsang, A. (2009) 'Comparative assessment of DNA assemblers for assembling expressed sequence tags', Ohio Collaborative Conf. Bioinform., Cleveland, Ohio, The IEEE Computer Society, pp.79-82.
10. Semova, N., Storms, R., John, T., Gaudet, P., Ulycznyj, P., Min, X.J., Sun, J., Butler, G. and Tsang, A. (2006) 'Generation, annotation, and analysis of an extensive Aspergillus niger EST collection', BMC Microbiol., Vol. 6, p.7.
11. Wang, B.B. and Brendel, V. (2006) Genomewide comparative analysis of alternative splicing in plants', Proc. Natl. Acad. Sci. USA, Vol. 103, pp.7175-7180.