Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania
1 Research Centre in Infectious Diseases, CHUL Research Centre, 2705 Laurier Blvd., Quebec, QC G1V 4G2, Canada
2 McGill Center for Bioinformatics, 3775 University St., Montreal, QC H3A 2B4, Canada
BMC Bioinformatics 2008, 9:158 doi:10.1186/1471-2105-9-158Published: 20 March 2008
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