Thank you for using SPLICE POA!
Please, reference our papers:


1. Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs.
Catherine Grasso, Barmak Modrek, Yi Xing & Christopher Lee
Pac Symp Biocomput. 2004:29-41.
2. Multiple Sequence Alignment Using Partial Order Graphs
Christopher Lee, Catherine Grasso, & Mark Sharlow
Bioinformatics 2002 18:452-464.

Download SPLICE POA   (updated 6-10-2004)

SPLICE POA Readme   (updated 3-15-2004)

SPLICE POA analyzes a multiple sequence alignment consisting of expressed sequences aligned to genomic to identify splices and exons. It was used to generate the data in ASAP, the Alternative Splicing Annotation Project Database, which is used by Yi Xing's mRNA and protein isoform generation program in generating the mRNAs and proteins in the ASP Alternatively Spliced Proteins Database.


The SPLICE POA program was written by Catherine Grasso as a set of library functions for the POA program, written by Christopher Lee.

Publications Using Data Generated By SPLICE POA
Resch, A., Xing, Y., Alekseyenko, A., Modrek, B., Lee, C. (2004) Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res. 32: 1261-9. [link]

Xing, Y., Resch, A., Lee, C. (2004) The Multiassembly Problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res. in press: . [link]

Grasso, C., Modrek, B., Xing, Y., Lee, C. (2004) Genome-wide detection of alternative-splicing in expressed sequences using partial order multiple sequence alignment graphs. Pac. Symp. Biocomputing World Scientific: Singapore, 29-41. [link]

Resch, A., Xing, Y., Modrek, B., Gorlick, M., Riley, R., Lee, C. (2004) Assessing the Impact of Alternative Splicing on Domain Interactions in the Human Proteome. J. Proteome Res. 32: 76-83. [link]

Xu, Q., Lee, C. (2003) Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res. 31: 5635-5643. [link]

Xing, Y., Xu, Q., Lee, C. (2003) Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains. FEBS Lett. 555: 572-8. [link]

Modrek, B., Lee, C. (2003) Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nature Genetics 34: 177-180. [link]

Lee, C., Irizarry, K. (2003) Alternative splicing in the nervous system: an emerging source of diversity and regulation. Biol. Psych. 54: 771-6. [link]

Lee, C., Atanelov, L., Modrek, B., Xing, Y. (2003) ASAP: The Alternative Splicing Annotation Project. Nucleic Acids Res. 31: 101-5. [link]

Xu, Q., Modrek, B., Lee, C. (2002) Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res. 30: 3754-66. [link]

Modrek, B., Resch, A., Grasso, C., Lee, C. (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Research 29: 2850-2859. [link]