Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania

doi:10.1186/1471-2105-9-158

BMC Bioinformatics

Volume 9

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Research article

Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania

Martin Smith¹^,2 , Mathieu Blanchette² and Barbara Papadopoulou¹

¹Research Centre in Infectious Diseases, CHUL Research Centre, 2705 Laurier Blvd., Quebec, QC G1V 4G2, Canada

²McGill Center for Bioinformatics, 3775 University St., Montreal, QC H3A 2B4, Canada

author email corresponding author email

BMC Bioinformatics 2008, 9:158doi:10.1186/1471-2105-9-158


Published:	20 March 2008

Additional files

Additional file 1:

Polyadenylated ESTs. PDF document of all 218 polyadenylated EST accession IDs used to build scanning matrices in this work.

Format: PDF Size: 50KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 2:

Over-represented hexamers. A Microsoft Word document containing the 10 highest scoring hexamers identified with YMF and FindExplanator programs. An alignment of 223 sequences was used to compare regions encompassing the [-125; +125] of genomic poly(A) sites to the [-800; -126] and [+126; +800] regions.

Format: DOC Size: 29KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional file 3:

PSSM scanning results for different matrix sizes and scanning distances. A Microsoft Excel spreadsheet containing all sensitivity results for single-matrix scanning approaches.

Format: XLS Size: 144KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 4:

PRED-A-TERM program. The prediction algorithm described in this manuscript has been implemented into a JAVA program which can be used to scan query sequences using any operating system. Once extracted, detailed usage instructions can be viewed in the README.txt file.

Format: ZIP Size: 268KB Download file