Research article
Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio
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* Corresponding author: Martin Kollmar mako@nmr.mpibpc.mpg.de
- † Equal contributors
1 Abteilung NMR basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany
2 Institute of Computer Science, University of Göttingen, Goldschmidtstr. 7, 37077 Göttingen, Germany
BMC Research Notes 2011, 4:265 doi:10.1186/1756-0500-4-265
Published: 28 July 2011Additional files
Additional file 1:
Activity flow of the hit processing step. The scheme shows a detailed activity flow of the hit processing step. Here, the experienced user can see, where and how the various expert parameters modulate Scipio's hit processing, and can thus adjust these parameters to get the best result possible.
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Additional file 2:
Protein - DNA alignments corresponding to the example searches. Here, additional data corresponding to the example searches is provided.
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Additional file 3:
Table with detailed data of the results of the cross-species search of the human DHC genes in the elephant genome. The table provides detailed data to the cross-species searches including numbers of matches and mismatches, gaps and intron?'s, for the searches with different parameters.
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Additional file 4:
Detailed evaluation values used for Tables 2, 3, and 4. This file provides a description of each evaluation parameter and the values obtained with each software tool for all sequence predictions. The values highlighted in yellow were used for Tables 2, 3, and 4.
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Additional file 5:
Software versions and run parameters of the gene reconstruction and prediction tools. The tables shows the exact versions and run parameters, which were used for the comparison, for each scenario.
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