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Open Access Research article

Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features

Andrew S Peek

Author Affiliations

Department of Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 52241, USA

BMC Bioinformatics 2007, 8:182  doi:10.1186/1471-2105-8-182

Published: 6 June 2007

Additional files

Additional file 1:

suppl1_comparison_position_specific_base_composition. Sites and bases within the guide strand found from several studies and datasets to be either significant or not significant in their influence of RNAi activity.

Format: XLS Size: 31KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

suppl2_all_features_corr_descr_tval. Features with their associated descriptions, correlations with RNAi activity and t-test values of significance.

Format: TXT Size: 196KB Download file

Open Data

Additional file 3:

supplementary_figure_1. The base composition bias within the localized target site of the siRNA guide strand, for 100 bases upstream and downstream of the guide strand target area.

Format: PDF Size: 253KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4:

supplementary_figure_2. The base composition bias within the localized target site of the siRNA guide strand, for 21 bases upstream and downstream of the guide strand target area.

Format: PDF Size: 229KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

tr_2431_cfsfilters. The features found to be useful by Correlation based Feature in training and testing the 2431 dataset by cross validation, at t-test values from 0 to 90.

Format: GZ Size: 2.2MB Download file

Open Data

Additional file 6:

tr_579_cfsfilters. The features found to be useful by Correlation based Feature in training and testing the 579 dataset by cross validation, at t-test values from 0 to 90.

Format: GZ Size: 3.1MB Download file

Open Data

Additional file 7:

seq2svm_0.3. An GNU platform deployable GPL code base for performing SVM modeling on small RNA sequences, with examples. Deploy by unzipping, untarring, and building with configure and make. See the included readme files. Updated versions will be available at ftp://scitoolsftp.idtdna.com/SEQ2SVM/ webcite.

Format: GZ Size: 8.9MB Download file

Open Data