-
Notifications
You must be signed in to change notification settings - Fork 60
/
Copy pathss_gd_align.html
295 lines (262 loc) · 8.5 KB
/
ss_gd_align.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
<html>
<head>
<title>
SS_GD_ALIGN - Sequence/sequence Global Distance Alignment
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
SS_GD_ALIGN <br> Sequence/sequence Global Distance Alignment
</h1>
<hr>
<p>
<b>SS_GD_ALIGN</b>
is a FORTRAN90 library which
implements some of the string
matching algorithms described in the reference <b>[Chao]</b>.
</p>
<p>
A global
alignment is attempted between the strings, and similarity is measured by
a sort of distance. These algorithms carry out the computation in
<I>linear space</I>, and compute not just the optimal alignment
score, but the corresponding optimal alignment.
</p>
<p>
It's important to be able to compute alignments using "linear space",
that is, just a few vectors whose length <b>N</b> is equal to that
of a typical string. A quadratic algorithm would require a two
dimensional array of total dimension <b>N*N</b>. Realistic alignment
problems can involve strings of <b>N</b>=100,000 elements or more,
so a quadratic algorithm would be expensive or impossible to use.
</p>
<p>
The score for the actual best matching is determined without
constructing the best matching, and in fact it is a matter of some
difficulty to recover the matching, particularly if the algorithm is a
linear space one, which discards a great deal of intermediate information.
However, a linear space algorithm included here can also compute the
optimal matching, based on the idea of a recursive subdivision of the
problem.
</p>
<p>
Routines that use quadratic space are included as well, so the algorithms
can be compared for storage, speed, and correctness.
</p>
<h3 align = "center">
Licensing:
</h3>
<p>
The computer code and data files described and made available on this web page
are distributed under
<a href = "../../txt/gnu_lgpl.txt">the GNU LGPL license.</a>
</p>
<h3 align = "center">
Related Data and Programs:
</h3>
<p>
<a href = "../../f_src/ps_gg_align/ps_gg_align.html">
PS_GG_ALIGN</a>,
a FORTRAN90 library which
implements a profile/sequence global alignment using an affine gap penalty.
</p>
<p>
<a href = "../../f_src/ps_lg_align/ps_lg_align.html">
PS_LG_ALIGN</a>,
a FORTRAN90 library which
implements a profile/sequence local alignment using an affine gap penalty.
</p>
<p>
<a href = "../../f_src/ps_qg_align/ps_qg_align.html">
PS_QG_ALIGN</a>,
a FORTRAN90 library which
implements a profile/sequence quasiglobal alignment using an affine gap penalty.
</p>
<p>
<a href = "../../f_src/ss_gg_align/ss_gg_align.html">
SS_GG_ALIGN</a>,
a FORTRAN90 library which
globally aligns two sequences using an affine gap penalty.
</p>
<p>
<a href = "../../f_src/ss_lg_align/ss_lg_align.html">
SS_LG_ALIGN</a>,
a FORTRAN90 library which
locally aligns two sequences using an affine gap penalty.
</p>
<p>
<a href = "../../f_src/ss_qg_align/ss_qg_align.html">
SS_QG_ALIGN</a>,
a FORTRAN90 library which
quasi-globally aligns two sequences using an affine gap penalty.
</p>
<h3 align = "center">
Reference:
</h3>
<p>
<ol>
<li>
Kun-Mao Chao, Ross Hardison, Webb Miller,<br>
Recent Developments in Linear-Space Alignment Methods: A Survey,<br>
Journal of Computational Biology, <br>
Volume 1, Number 4, 1994, pages 271-291.
</li>
<li>
Eugene Myers, Webb Miller,<br>
Optimal Alignments in Linear Space,<br>
CABIOS,<br>
Volume 4, number 1, 1988, pages 11-17.
</li>
<li>
Michael Waterman,<br>
Introduction to Computational Biology,<br>
Chapman and Hall, 1995,<br>
ISBN: 0412993910,<br>
LC: QH438.4.M33.W38.
</li>
</ol>
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
<ul>
<li>
<a href = "ss_gd_align.f90">ss_gd_align.f90</a>, the source code;
</li>
<li>
<a href = "ss_gd_align.sh">ss_gd_align.sh</a>,
commands to compile the source code;
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<ul>
<li>
<a href = "ss_gd_align_prb.f90">ss_gd_align_prb.f90</a>, test global
distance routines;
</li>
<li>
<a href = "ss_gd_align_prb.sh">ss_gd_align_prb.sh</a>,
commands to compile, link and run the sample problem;
</li>
<li>
<a href = "ss_gd_align_prb_output.txt">ss_gd_align_prb_output.txt</a>, the global
distance test output.
</li>
</ul>
</p>
<h3 align = "center">
List of Routines:
</h3>
<p>
<ul>
<li>
<b>A_INDEX</b> sets up a reverse index for the amino acid codes.
</li>
<li>
<b>A_TO_I4</b> returns the index of an alphabetic character.
</li>
<li>
<b>CH_CAP</b> capitalizes a single character.
</li>
<li>
<b>CHVEC2_PRINT</b> prints two vectors of characters.
</li>
<li>
<b>I4_SWAP</b> switches two integer values.
</li>
<li>
<b>I4_TO_A</b> returns the I-th alphabetic character.
</li>
<li>
<b>I4VEC2_COMPARE</b> compares pairs of integers stored in two vectors.
</li>
<li>
<b>I4VEC2_PRINT</b> prints a pair of integer vectors, with an optional title.
</li>
<li>
<b>I4VEC2_SORT_A</b> ascending sorts a vector of pairs of integers.
</li>
<li>
<b>I4VEC_REVERSE</b> reverses the elements of an integer vector.
</li>
<li>
<b>PAM120</b> returns the PAM 120 substitution matrix.
</li>
<li>
<b>PAM120_SCORE</b> computes a single entry sequence/sequence matching score.
</li>
<li>
<b>PAM200</b> returns the PAM 200 substitution matrix.
</li>
<li>
<b>PAM200_SCORE</b> computes a single entry sequence/sequence matching score.
</li>
<li>
<b>RVEC2_SUM_IMAX</b> returns the index of the maximum sum of two real vectors.
</li>
<li>
<b>S_EQI</b> is a case insensitive comparison of two strings for equality.
</li>
<li>
<b>S_TO_CVEC</b> converts a string to a character vector.
</li>
<li>
<b>S_TO_I4</b> reads an integer value from a string.
</li>
<li>
<b>SIMPLE_SCORE</b> computes a single entry sequence/sequence matching score.
</li>
<li>
<b>SORT_HEAP_EXTERNAL</b> externally sorts a list of items into linear order.
</li>
<li>
<b>SS_GD_BPQ</b> does a global distance backward alignment path in quadratic space.
</li>
<li>
<b>SS_GD_BSL</b> does a global distance backward alignment score in linear space.
</li>
<li>
<b>SS_GD_BSQ</b> does a global distance backward alignment score in quadratic space.
</li>
<li>
<b>SS_GD_FPQ</b> does a global distance forward alignment path in quadratic space.
</li>
<li>
<b>SS_GD_FSL</b> does a global distance forward alignment score in linear space.
</li>
<li>
<b>SS_GD_FSQ</b> does a global distance forward alignment score in quadratic space.
</li>
<li>
<b>SS_GD_MATCH_PRINT</b> prints a global distance alignment.
</li>
<li>
<b>SS_GD_RPL</b> does a global distance recursive alignment path in linear space.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
<li>
<b>WORD_LAST_READ</b> returns the last word from a string.
</li>
<li>
<b>WORD_NEXT_READ</b> "reads" words from a string, one at a time.
</li>
</ul>
</p>
<p>
You can go up one level to <a href = "../f_src.html">
the FORTRAN90 source codes</a>.
</p>
<hr>
<i>
Last revised on 20 January 2011.
</i>
<!-- John Burkardt -->
</body>
</html>