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Open Access Research article

A method for identifying alternative or cryptic donor splice sites within gene and mRNA sequences. Comparisons among sequences from vertebrates, echinoderms and other groups

Katherine M Buckley13, Liliana D Florea24 and L Courtney Smith1*

Author Affiliations

1 The Department of Biological Sciences, Washington University, Washington, DC 20052, USA

2 The Department of Computer Science, George, Washington University, Washington, DC 20052, USA

3 Current address : Department of Immunology, University of Toronto, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, Ontario, M4N 3M5, Canada

4 Current address : Center for Bioinformatics and Computational Biology, University of Maryland 3119 Biomolecular Sciences Bldg (#296), College Park, MD 20742, USA

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BMC Genomics 2009, 10:318  doi:10.1186/1471-2164-10-318

Published: 16 July 2009

Additional files

Additional file 1:

Representative 185/333 element patterns. An illustration, modified from [23] that illustrates the element patterns of the 185/333 messages and the locations of the putative donor splice sites.

Format: DOCX Size: 62KB Download file

Open Data

Additional file 2:

Vertebrate sequence accession numbers. An Excel spreadsheet containing the accession numbers of the vertebrate sequences used to evaluate the splicing models.

Format: XLS Size: 455KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Protostome sequence accession numbers. An Excel spreadsheet containing the accession numbers of the protostome sequences used to evaluate the splicing models.

Format: XLS Size: 320KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Echinoderm sequence accession numbers. An Excel spreadsheet containing the accession numbers of the experimentally validated echinoderm sequences used to evaluate the splicing models.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Purpuratus splicer. A PERL script to implement the Purpuratus splicing model.

Format: TXT Size: 16KB Download file

Open Data

Additional file 6:

Vertebrate splicer. A PERL script to implement the Vertebrate splicing model.

Format: TXT Size: 11KB Download file

Open Data