📄 第三章.htm
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<p class=MsoPlainText style='text-indent:21.25pt;line-height:150%'><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt'>很显然，在比较两条序列<span lang=EN-US>s和t时，在s中的一个删除操作等价于在t中对应位置上的一个插入操作，反之亦然。需要注意的是，两个空位字符不能匹配，因为这样的操作没有意义。引入上述编辑操作后，重新计算两条序列的距离，就成为编辑距离。</span></span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText style='text-indent:21.25pt;line-height:150%'><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt'>以上的操作仅仅是关于序列的常用操作，在实际应用中还可以引入复杂的序列操作。下面是两条序列的一种比对：</span><span
lang=EN-US><o:p></o:p></span></p>
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<p class=MsoPlainText style='text-indent:21.25pt;line-height:150%'><span
style='font-size:10.0pt'>上述比对不能反映两条序列的本质关系。但是，如果将第二条序列头尾倒置，可以发现两条序列惊人的相似：</span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span lang=EN-US><!--[if gte vml 1]><v:shape id="_x0000_i1031"
type="#_x0000_t75" alt="" style='width:143.25pt;height:47.25pt'>
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src="./第三章.files/image014.jpg" v:shapes="_x0000_i1031"><![endif]><o:p></o:p></span></p>
<p class=MsoPlainText style='text-indent:21.25pt;line-height:150%'><span
style='font-size:10.0pt'>再比如，下面两条序列有什么关系？如果将其中一条序列中的碱基替换为其互补碱基，就会发现其中的关系：</span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span lang=EN-US style='font-size:10.0pt'>CTAGTCGAGGCAATCT<O:P>
</O:P></span><span lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span lang=EN-US style='font-size:10.0pt'>GAACAGCTTCGTTAGT</span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span lang=EN-US><!--[if gte vml 1]><v:shape id="_x0000_i1032"
type="#_x0000_t75" alt="" style='width:386.25pt;height:196.5pt'>
<v:imagedata src="./第三章.files/image015.png" o:href="http://www.lmbe.seu.edu.cn/chenyuan/xsun/bioinfomatics/web/images/82.bmp"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=515 height=262
src="./第三章.files/image016.jpg" v:shapes="_x0000_i1032"><![endif]><O:P></O:P><o:p></o:p></span></p>
<p class=MsoPlainText style='line-height:150%'><b><span lang=EN-US
style='color:#EFCE8F'>3.1.3 通过点矩阵分析两条序列的相似之处 </span></b><span lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText style='text-indent:21.25pt;line-height:150%'><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt'>进行序列比较的一个简单的方法是<span
lang=EN-US>“矩阵作图法”或“对角线作图”，这种方法是由Gibb首先提出的。将两条待比较的序列分别放在矩阵的两个轴上，一条在X轴上，从左到右，一条在Y轴上，从下往上，如</span></span><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt;color:blue'>图<span
lang=EN-US>3.2</span></span><span style='font-size:10.0pt;mso-bidi-font-size:
10.5pt'>所示。当对应的行与列的序列字符匹配时，则在矩阵对应的位置作出<span lang=EN-US>“点”标记。逐个比较所有的字符对，最终形成点矩阵。</span></span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span lang=EN-US><!--[if gte vml 1]><v:shape id="_x0000_i1033"
type="#_x0000_t75" alt="" style='width:207.75pt;height:89.25pt'>
<v:imagedata src="./第三章.files/image017.png" o:href="http://www.lmbe.seu.edu.cn/chenyuan/xsun/bioinfomatics/web/images/83.bmp"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=277 height=119
src="./第三章.files/image018.jpg" v:shapes="_x0000_i1033"><![endif]><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span style='font-size:10.0pt;mso-bidi-font-size:10.5pt'>图<span
lang=EN-US>3.2 序列比较矩阵标记图</span></span><span lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText style='text-indent:21.25pt;line-height:150%'><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt'>显然，如果两条序列完全相同，则在点矩阵主对角线的位置都有标记；如果两条序列存在相同的子串，则对于每一个相同的子串对，有一条与对角线平行的由标记点所组成的斜线，如</span><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt;color:blue'>图<span
lang=EN-US>3.3</span></span><span style='font-size:10.0pt;mso-bidi-font-size:
10.5pt'>中的斜线代表相同的子串<span lang=EN-US>“ATCC”；而对于两条互为反向的序列，则在反对角线方向上有标记点组成的斜线，如</span></span><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt;color:blue'>图<span
lang=EN-US>3.4</span></span><span style='font-size:10.0pt;mso-bidi-font-size:
10.5pt'>所示。</span><span lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span lang=EN-US><!--[if gte vml 1]><v:shape id="_x0000_i1034"
type="#_x0000_t75" alt="" style='width:266.25pt;height:117.75pt'>
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</v:shape><![endif]--><![if !vml]><img border=0 width=355 height=157
src="./第三章.files/image020.jpg" v:shapes="_x0000_i1034"><![endif]><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span style='font-size:10.5pt;mso-bidi-font-size:10.0pt;
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-font-kerning:1.0pt'>图</span><span lang=EN-US style='font-size:10.5pt;
mso-bidi-font-size:10.0pt;font-family:"Times New Roman";mso-font-kerning:1.0pt'>3.3<span
style="mso-spacerun: yes"> </span></span><span style='font-size:10.5pt;
mso-bidi-font-size:10.0pt;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
"Times New Roman";mso-font-kerning:1.0pt'>相同子串矩阵标记图</span><span lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span lang=EN-US><!--[if gte vml 1]><v:shape id="_x0000_i1035"
type="#_x0000_t75" alt="" style='width:177.75pt;height:93.75pt'>
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</v:shape><![endif]--><![if !vml]><img border=0 width=237 height=125
src="./第三章.files/image022.jpg" v:shapes="_x0000_i1035"><![endif]><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span style='font-size:10.5pt;mso-bidi-font-size:10.0pt;
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-font-kerning:1.0pt'>图</span><span lang=EN-US style='font-size:10.5pt;
mso-bidi-font-size:10.0pt;font-family:"Times New Roman";mso-font-kerning:1.0pt'>3.4<span
style="mso-spacerun: yes"> </span></span><span style='font-size:10.5pt;
mso-bidi-font-size:10.0pt;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
"Times New Roman";mso-font-kerning:1.0pt'>反向序列矩阵标记图</span><span lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText style='text-indent:21.25pt;line-height:150%'><span
style='font-size:10.0pt;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
"Times New Roman"'>对于矩阵标记图中非重叠的与对角线平行斜线，可以组合起来，形成两条序列的一种比对。在两条子序列的中间可以插入符号“</span><span
lang=EN-US style='font-size:10.0pt'>-</span><span style='font-size:10.0pt;
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman"'>”，表示插入空位字符。在这种对比之下分析两条序列的相似性，如</span><span
style='font-size:10.0pt;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
"Times New Roman";color:blue'>图</span><span lang=EN-US style='font-size:10.0pt;
color:blue'>3.5</span><span style='font-size:10.0pt;mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman"'>所示。找两条序列的最佳比对（对应位置等同字符最多），实际上就是在矩阵标记图中找非重叠平行斜线最长的组合。</span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span lang=EN-US><!--[if gte vml 1]><v:shape id="_x0000_i1036"
type="#_x0000_t75" alt="" style='width:311.25pt;height:130.5pt'>
<v:imagedata src="./第三章.files/image023.png" o:href="http://www.lmbe.seu.edu.cn/chenyuan/xsun/bioinfomatics/web/images/86.bmp"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=415 height=174
src="./第三章.files/image024.jpg" v:shapes="_x0000_i1036"><![endif]><o:p></o:p></span></p>
<p class=MsoPlainText align=center style='text-align:center;text-indent:21.25pt;
line-height:150%'><span style='font-size:10.5pt;mso-bidi-font-size:10.0pt;
mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
mso-font-kerning:1.0pt'>图</span><span lang=EN-US style='font-size:10.5pt;
mso-bidi-font-size:10.0pt;font-family:"Times New Roman";mso-font-kerning:1.0pt'>3.5<span
style="mso-spacerun: yes"> </span></span><span style='font-size:10.5pt;
mso-bidi-font-size:10.0pt;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
"Times New Roman";mso-font-kerning:1.0pt'>多个相同连续子序列矩阵标记图</span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
text-indent:21.25pt;line-height:150%'><span style='font-size:10.0pt;mso-bidi-font-size:
10.5pt;font-family:宋体;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
"Times New Roman"'>除非已经知道待比较的序列非常相似，一般先用点矩阵方法比较，因为这种方法可以通过观察矩阵的对角线迅速发现可能的序列比对。</span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
text-indent:21.25pt;line-height:150%'><b><span style='font-size:10.0pt;
mso-bidi-font-size:10.5pt;font-family:宋体;mso-ascii-font-family:"Times New Roman";
mso-hansi-font-family:"Times New Roman"'>实例</span></b><b><span lang=EN-US
style='font-size:10.0pt;mso-bidi-font-size:10.5pt'>1</span></b><b><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt;font-family:宋体;mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman"'>：</span></b><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal align=center style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;text-align:center;text-indent:21.25pt;line-height:150%'><span lang=EN-US
style='font-size:10.0pt;mso-bidi-font-size:10.5pt'><!--[if gte vml 1]><v:shape
id="_x0000_i1037" type="#_x0000_t75" alt="" style='width:251.25pt;height:251.25pt'>
<v:imagedata src="./第三章.files/image025.png" o:href="http://www.lmbe.seu.edu.cn/chenyuan/xsun/bioinfomatics/web/images/87.bmp"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=335 height=335
src="./第三章.files/image026.jpg" v:shapes="_x0000_i1037"><![endif]></span><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal align=left style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;text-align:left;text-indent:21.25pt;line-height:150%'><b><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt;font-family:宋体;mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman"'>实例</span></b><b><span
lang=EN-US style='font-size:10.0pt;mso-bidi-font-size:10.5pt'>2</span></b><b><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt;font-family:宋体;mso-ascii-font-family:
"Times New Roman";mso-hansi-font-family:"Times New Roman"'>：</span></b><span
lang=EN-US><o:p></o:p></span></p>
<p class=MsoNormal align=center style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;text-align:center;text-indent:21.25pt;line-height:150%'><span lang=EN-US><!--[if gte vml 1]><v:shape
id="_x0000_i1038" type="#_x0000_t75" alt="" style='width:258.75pt;height:276.75pt'>
<v:imagedata src="./第三章.files/image027.png" o:href="http://www.lmbe.seu.edu.cn/chenyuan/xsun/bioinfomatics/web/images/88.bmp"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=345 height=369
src="./第三章.files/image028.jpg" v:shapes="_x0000_i1038"><![endif]><O:P></O:P><o:p></o:p></span></p>
<p class=MsoNormal align=left style='mso-margin-top-alt:auto;mso-margin-bottom-alt:
auto;text-align:left;text-indent:21.25pt;line-height:150%'><span
style='font-size:10.0pt;mso-bidi-font-size:10.5pt;font-family:宋体;mso-ascii-font-family:
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