Online
|
Download
|
Store
|
Contact
|
About

SVM SeqClassifier 1.2: Train Your Sequences To Learn           Order Home
   Support Vector Machine (SVM) is one of the best statistical learning methods. The SVM Classifier 1.2 and SVM SeqClassifier 1.2 are based on JAVA Implementation of LIBSVM, a simplified form of SVM. The goal is to provide biologists a friendly tool to test their hypothesis without the need of programming. Users may find the light version satisfactory for many applications.
  • SeqClassifier --- DNA / Protein sequence data
  • SVM Classifier --- numerical data.
    Order SVM SeqClassifier
    Countersince 3/25/03
  • SVM Online runs on Java-enabled browsers
    PC: Internet Explorer 5.5 or higher and Netscape 4.08 or higher
    Mac: Internet Explorer 5.0, IE5.1.4 or higher (IE5.1 will not work because of a bug.)
    Need to raise a better antibody?
    Please use online Abie Pro 3.0 for
    peptide antibody design.

    The Electronic Protocol Book Table of contents BioToolKit 300 Download Trials
         An electronic protocol book with 500 protocols and 100 recipes. A great quick and practical reference for bench scientists as well as for new students.   Get A Copy      A collection of tools frequently used by bench biomedical scientists, ranging from centrifugation force conversion, molecular weight, OD, recipe calculators, to clinical calculators. Include all Primo 3.4, Abie 3.0, Heatmap Viewer, MicroHelper, Godlist Manager, label printing, and grade book.   More info
    SVM links
    Support Vector Machines Online Machine Learning
    Machine Learning Resources SVM Applications in Biology
    Example III: Prediction of Splice Sites
    Test Drive SVM SeqClassifier 1.2
    1. Click here to download the training data.
    2. Select the data, copy (Ctrl-c or Apple-c) and paste (Ctrl-v or Apple-v) into the training data input window (top-left) of the SVM SeqClassifier 1.2.
    The input data file should have the following format:
    3. Select model, kernel, and whether to scale the data. If the scale is checked, each row will be scaled internally (should not make big differences for SeqClassifier whether the data is scaled or not).
    4. Click on the Train button to train a model.
    5. Click here to download the testing data.
    6. Select the data, copy (Ctrl-c or Apple-c) and paste (Ctrl-v or Apple-v) into the testing data input window (top-right) of the SVM SeqClassifier 1.2.
    7. Click on the Predict button to predict.
    8. Click on the Validate button to run cross-validation.

    Warning: Due to limit of your clip board memory, it is impossible to copy/paste a large dataset. You would need the Stand-alone version, which allows data upload.

    Data
    The data for this demo is the human 5'-splice site used in the GENIE system. Additional data can be found at Berkeley Drosophila Genome Project. For the demo purpose, the first 100 true and first 200 false 5'-donor sequences from training or testing sets are used.

    Example IV: Just for Fun
    +1	--Chemomics
    +1	-proteomics
    +1	---genomics
    +1	-Agronomics
    +1	--bionomics
    -1	-deadnomics
    -1	bushonomics
    -1	Reidonomics
    -1	Urbannomics
    -1	-EekANomics
    -1	-Ragonomics
    -1	-eekanomics
    -1	-firenomics
    -1	-ergonomics
    -1	-Oeconomics
    -1	Phoronomics
    -1	-Pyronomics
    -1	Loxodromics
    -1	Bubbleomics
    -1	-Enronomics
    -1	-optinomics
    -1	--economics
    -1	--netnomics
    -1	ARMEYNOMICS
    
    Copy and paste the "omics" data into the SeqClassifier, and try to find the the best model for predicting next "true omics" related to biology.
    SVM SeqClassifier is designed as a flexible, light-weight and user-friendly Classifier. For most dataset with tens to hundreds of training and testing sequences, it should finish reasonably fast on personal computers. For large dataset with thousands of sequences, SeqClassifier may need to be modified. Please contact us for details.
    Example V: siRNA Design
    Click here to see how SVM can be applied to select for siRNA.


    What is a USB Flash Disk?

    Home Products Order Contact

    THIS SOFTWARE IS PROVIDED BY CHANG BIOSCIENCE ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL CHANG BIOSCIENCE OR ITS SPONSORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


    Copyright 2002-2004 Chang Bioscience, Inc. All rights reserved.