風吹乾了我就走

SOV(segment overlap)是測量預測蛋白質二級體結構的一種方法

跟Q3的方法不同的是以片段的觀念比較

以下用例子說明：

假設有一條蛋白質結構為：CCHHHHHCCCCCCCHHHHHHHHCHHHHHHHHCCCC

預測出來的結果為：           CCHCHCHCCCCCCCCHCHCHCHCHHHCHHHHCCCC

以Q3來測量為 28 / 35 = 80%(一般而言Q3大於70%就是相當不錯的預結果)

但實際上蛋白質二級體結構並不會出現單一helix這種結構

用Q3來測量並不能符合需求，所以才產生SOV的方法。

 

詳細的SOV的公式和介紹請參考：

1.A modified Definition of Sov, a Segment-Based Measure for Protein Secondary Structure Prediction Assessment.(Adam Zemla etc al., PROTEINS:Structure,Function,and Genetics 34:220-223, 1999)

2.EVA measures for secondary structure prediction accuracy

 

SOV和Q3都是常見到的方法，但網路上似乎沒有找到有人寫好的Code(或許是我找不到吧)，雖然有一個server(SOV - segment overlap measure)提供SOV的計算但它有長度的限制，所以我有寫一個SOV JAVA的class，給各位參考一下，有需要的人也可以拿去用，但小弟是JAVA coding的新手，沒有寫的很好請多多包涵。

使用方法
SOV sov = new SOV(observedString, predictedString);
sov.getScore();

Code:

01 
02 
03 public class SOV {
04 
05     /** Observed */
06     private String[] ObsHStart;
07     private String[] ObsHEnd;
08 
09 
10     private String[] ObsEStart;
11     private String[] ObsEEnd;
12 
13     private String[] ObsCStart;
14     private String[] ObsCEnd;
15 
16     /** Predicted */
17     private String[] preHStart;
18     private String[] preHEnd;
19 
20     private String[] preEStart;
21     private String[] preEEnd;
22 
23     private String[] preCStart;
24     private String[] preCEnd;
25 
26     public SOV(String observedSeq, String predictedSeq) {
27         String[] temp = stringArray(observedSeq,'H').split(":");
28         if (temp.length > 0) {
29             ObsHStart = temp[0].split(",");
30             ObsHEnd = temp[1].split(",");
31         } else {
32             ObsHStart = null;
33             ObsHEnd = null;
34         }
35 
36         temp = stringArray(observedSeq,'E').split(":");
37         if (temp.length > 0) {
38             ObsEStart = temp[0].split(",");
39             ObsEEnd = temp[1].split(",");
40         } else {
41             ObsEStart = null;
42             ObsEEnd = null;
43         }
44 
45         temp = stringArray(observedSeq,'C').split(":");
46         if (temp.length > 0) {
47             ObsCStart = temp[0].split(",");
48             ObsCEnd = temp[1].split(",");
49         } else {
50             ObsCStart = null;
51             ObsCEnd = null;
52         }
53 
54         temp = stringArray(predictedSeq,'H').split(":");
55         if (temp.length > 0) {
56             preHStart = temp[0].split(",");
57             preHEnd = temp[1].split(",");
58         } else {
59             preHStart = null;
60             preHEnd = null;
61         }
62 
63         temp = stringArray(predictedSeq,'E').split(":");
64         if (temp.length > 0) {
65             preEStart = temp[0].split(",");
66             preEEnd = temp[1].split(",");
67         } else {
68             preEStart = null;
69             preEEnd = null;
70         }
71 
72         temp = stringArray(predictedSeq,'C').split(":");
73         if (temp.length > 0) {
74             preCStart = temp[0].split(",");
75             preCEnd = temp[1].split(",");
76         } else {
77             preCStart = null;
78             preCEnd = null;
79         }
80     }
81 
82     public double getScore() {
83         double HsegmentValue = function(ObsHStart, ObsHEnd, preHStart, preHEnd);
84         double EsegmentValue = function(ObsEStart, ObsEEnd, preEStart, preEEnd);
85         double CsegmentValue = function(ObsCStart, ObsCEnd, preCStart, preCEnd);
86         double segmentSum = HsegmentValue + EsegmentValue + CsegmentValue;
87 
88         int HValue = NValue(ObsHStart, ObsHEnd, preHStart, preHEnd);
89         int EValue = NValue(ObsEStart, ObsEEnd, preEStart, preEEnd);
90         int CValue = NValue(ObsCStart, ObsCEnd, preCStart, preCEnd);
91         int NSum = HValue + EValue + CValue;
92 
93         return (double)100 / NSum * segmentSum;
94     }
95 
96     private String stringArray(String sequence, char ch) {
97         char[] seqArray = sequence.toCharArray();
98         StringBuilder start = new StringBuilder();
99         StringBuilder end = new StringBuilder();
100 
101         for (int count = 0; count < seqArray.length; count++) {
102             if (seqArray[count] == ch) {
103                 start.append(count).append(',');
104                 while (seqArray[count] == ch) {
105                     if (count == seqArray.length - 1) {
106                         count++;
107                         break;
108                     }
109                     count++;
110                 }
111                 end.append(count - 1).append(',');
112             }
113         }
114         start.append(':').append(end.toString());
115         return start.toString();
116 
117     }
118 
119     private double function(String[] obsStart, String[] obsEnd, String[] preStart, String[] preEnd) {
120         if (obsStart == null || preStart == null) return 0.0;
121         int oStart, oEnd, pStart, pEnd, start, end;
122         int minov, maxov, delta, s1Length, s2Length;
123         double funcSum = 0.0;
124         for (int count = 0; count < obsStart.length; count++) {
125             oStart = Integer.parseInt(obsStart[count]);
126             oEnd = Integer.parseInt(obsEnd[count]);
127 
128             for (int count2 = 0; count2 < preStart.length; count2++) {
129                 pStart = Integer.parseInt(preStart[count2]);
130                 pEnd = Integer.parseInt(preEnd[count2]);
131 
132                 if ( (pStart >= oStart && pStart <= oEnd) || (pEnd >= oStart && pEnd  <= oEnd) ) {
133                     if ( pStart >= oStart )
134                         start = oStart;
135                     else start = pStart;
136 
137                     if ( pEnd >= oEnd )
138                         end = pEnd;
139                     else end = oEnd;
140                     maxov = end - start + 1;
141 
142                     if ( pStart >= oStart )
143                         start = pStart;
144                     else start = oStart;
145 
146                     if ( pEnd >= oEnd )
147                         end = oEnd;
148                     else end = pEnd;
149                     minov = end - start + 1;
150 
151                     s1Length = oEnd - oStart + 1;
152                     s2Length = pEnd - pStart + 1;
153 
154                     funcSum += (double)(minov + DELTA(maxov, minov, s1Length, s2Length)) / maxov * s1Length;
155                 }
156             }
157         }
158         return funcSum;
159     }
160 
161     private int DELTA(int maxov, int minov, int s1Length, int s2Length) {
162         int min, min2;
163         if (maxov - minov <= minov)
164             min = maxov - minov;
165         else min = minov;
166 
167         if ((int)s1Length / 2  <= (int)s2Length / 2)
168             min2 = (int)s1Length / 2;
169         else min2 = (int)s2Length / 2;
170 
171         if (min <= min2)
172             return min;
173         else return min2;
174     }
175 
176     private int NValue(String[] obsStart, String[] obsEnd, String[] preStart, String[] preEnd) {
177         if (obsStart == null || preStart == null) return 0;
178         int oStart, oEnd, pStart, pEnd;
179         int sum = 0;
180         for (int count = 0; count < obsStart.length; count++) {
181             int overlapCount = 0;
182             oStart = Integer.parseInt(obsStart[count]);
183             oEnd = Integer.parseInt(obsEnd[count]);
184 
185             for (int count2 = 0; count2 < preStart.length; count2++) {
186                 pStart = Integer.parseInt(preStart[count2]);
187                 pEnd = Integer.parseInt(preEnd[count2]);
188 
189                 if ( (pStart >= oStart && pStart <= oEnd) || (pEnd >= oStart && pEnd  <= oEnd) ) {
190                     sum += oEnd - oStart + 1;
191                     overlapCount++;
192                 }
193             }
194             if (overlapCount == 0)
195                 sum += oEnd - oStart + 1;
196         }
197 
198         return sum;
199     }
200 }
201