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
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
|
vectorstrip
Function
Strips out DNA between a pair of vector sequences
Description
vectorstrip is intended to be useful for stripping vector sequence
from the ends of sequences of interest. For example, if a fragment has
been cloned into a vector and then sequenced, the sequence may contain
vector data eg from the cloning polylinker at the 5' and 3' ends of
the sequence. vectorstrip will remove these contaminating regions and
output trimmed sequence ready for input into another application.
vectorstrip is suitable for use with low quality sequence data as it
can allow for mismatches between the sequence and the vector patterns
provided. You can specify the maximum level of mismatch expected.
Vector data can either be provided in a file or interactively. If
presented in a file, vectorstrip will search all input sequences with
all vectors listed in that file. The intention is that the user can
maintain a single file for use with vectorstrip, containing all the
linker sequences commonly used in the laboratory.
The two patterns for each vector are searched separately against the
sequence. Once the search is completed, each of the hits of the 5'
sequence is paired with each of the hits of the 3' sequence and the
resulting subsequences are output. For example, if the 5' sequence
matches the sequence from (a) position 30-60, and(b)position 70-100,
and the 3' sequence matches from 150-175, then two subsequences will
be output: from 61-149, and from 101-149. The lower the quality of the
sequence, the more likely multiple hits become if nonzero mismatches
are accepted.
Default behaviour is to report only the best matches between the
vector patterns and the sequence. This means that if you specify a
maximum mismatch level of 10%, but the vector patterns match the
sequence with zero mismatches, the search will stop and the program
will output only these "best" matches. If there are no perfect
matches, the program will try searching again allowing 1 mismatch,
then 2, and so on until either the patterns match the sequence or the
maximum specified mismatch level is exceeded. You can tell vectorstrip
to show all possible matches up to your specified maximum level, as
illustrated in the examples below.
Usage
Here is a sample session with vectorstrip
% vectorstrip @vecseqs.list
Strips out DNA between a pair of vector sequences
Are your vector sequences in a file? [Y]:
Cloning vector definition file (optional): vectors
Max allowed % mismatch [10]:
Show only the best hits (minimise mismatches)? [Y]:
Output file [pbluescript.vectorstrip]: vector.strip
output sequence(s) [pbluescript.fasta]: vector.fasta
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] seqall Nucleotide sequence(s) filename and optional
format, or reference (input USA)
[-[no]vectorfile] toggle [Y] Are your vector sequences in a file?
* -vectorsfile infile Cloning vector definition file (optional)
-mismatch integer [10] Max allowed % mismatch (Any integer
value)
-[no]besthits boolean [Y] Show only the best hits (minimise
mismatches)?
* -linkera string The 5' sequence (Any string is accepted)
* -linkerb string The 3' sequence (Any string is accepted)
[-outfile] outfile [*.vectorstrip] Output file name
[-outseq] seqoutall [.] Sequence set(s)
filename and optional format (output USA)
Additional (Optional) qualifiers:
-allsequences boolean [N] Show all sequences in output
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outfile" associated qualifiers
-odirectory3 string Output directory
"-outseq" associated qualifiers
-osformat4 string Output seq format
-osextension4 string File name extension
-osname4 string Base file name
-osdirectory4 string Output directory
-osdbname4 string Database name to add
-ossingle4 boolean Separate file for each entry
-oufo4 string UFO features
-offormat4 string Features format
-ofname4 string Features file name
-ofdirectory4 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
Input file format
Input files for usage example
File: vecseqs.list
../../data/bluescript.seq
../../data/litmus.seq
../../data/pTYB1.seq
File: vectors
# Example vector file for use by vectorstrip
# Vector 5' 3'
pTYB1 GACGGCGGCCGCGAATTCC TCGAGGGCTCTTCCTGC
pBS_KS+ GGGTACCGGGCCCCCCC TCGAGGTCGACGGTA
pLITMUS GATATCCTGCAGGAATTCC TCGAGACCGTACGTGCG
The same fragment has been cloned into the XhoI site of the polylinker
of each vector. The cloned fragment is represented in lower case and
the vector sequence in upper case so the sequence trimming can be
readily seen.
Each line of the vector file should contain the name of the vector,
the 5' pattern and the 3' pattern.
Lines beginning with # are treated as comments and ignored.
If only one vector sequence is given in the it will be assumed that
this is the 5' pattern.
If a vector name is given but no pattern data, the vector will not be
used.
Output file format
Output files for usage example
File: vector.strip
Sequence: pBlueScript Vector: pTYB1 No match
Sequence: pBlueScript Vector: pBS_KS+
5' sequence matches:
From 67 to 83 with 0 mismatches
3' sequence matches:
From 205 to 219 with 0 mismatches
Sequences output to file:
from 84 to 204
tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca
cacagtgacatgagagacacagatatagagacagatagacgatagacaga
cagcatatatagacagatagc
sequence trimmed from 5' end:
GGAAACAGCTAATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACT
AAAGGGAACAAAAGCTGGGTACCGGGCCCCCCC
sequence trimmed from 3' end:
TCGAGGTCGACGGTATCGATAAGCTTGATATCG
Sequence: pBlueScript Vector: pLITMUS No match
Sequence: litmus.seq Vector: pTYB1 No match
Sequence: litmus.seq Vector: pBS_KS+ No match
Sequence: litmus.seq Vector: pLITMUS
5' sequence matches:
From 43 to 61 with 0 mismatches
3' sequence matches:
From 183 to 199 with 0 mismatches
Sequences output to file:
from 62 to 182
tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca
cacagtgacatgagagacacagatatagagacagatagacgatagacaga
cagcatatatagacagatagc
sequence trimmed from 5' end:
TCTAGAACCGGTGACGTCTCCCATGGTGAAGCTTGGATCCACGATATCCT
GCAGGAATTCC
sequence trimmed from 3' end:
TCGAGACCGTACGTGCGCGCGAATGCATCCAGATCTTCCCTCTAGTCAAG
GCCTTAAGTGAGTCGTATTACGGA
Sequence: pTYB1.seq Vector: pTYB1
5' sequence matches:
From 40 to 58 with 0 mismatches
3' sequence matches:
From 180 to 196 with 0 mismatches
Sequences output to file:
from 59 to 179
tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagca
cacagtgacatgagagacacagatatagagacagatagacgatagacaga
cagcatatatagacagatagc
sequence trimmed from 5' end:
CTTTAAGAAGGAGATATACATATGGCTAGCTCGCGAGTCGACGGCGGCCG
CGAATTCC
sequence trimmed from 3' end:
TCGAGGGCTCTTCCTGCTTTGCCAAGGGTACCAATGTTTTAATGGCGGAT
Sequence: pTYB1.seq Vector: pBS_KS+ No match
Sequence: pTYB1.seq Vector: pLITMUS No match
File: vector.fasta
>pBlueScript_from_84_to_204 KS+
tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgaca
tgagagacacagatatagagacagatagacgatagacagacagcatatatagacagatag
c
>litmus.seq_from_62_to_182
tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgaca
tgagagacacagatatagagacagatagacgatagacagacagcatatatagacagatag
c
>pTYB1.seq_from_59_to_179
tcgagagccgtattgcgatatagcgcacatgcgttggacacagatgagcacacagtgaca
tgagagacacagatatagagacagatagacgatagacagacagcatatatagacagatag
c
Two types of output file are produced:
1. The sequence file(s) - contain the trimmed subsequence(s) produced
by vectorstrip either all in one file, or in separate files if the
command line flag -ossingle is used.
2. Results summary file
Data files
None.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
1.
No suitable vectors found - exiting
indicates that the 5' and 3' patterns for the vectors were blank -
usually this is as a result of an empty vectorfile.
2.
Illegal pattern
indicates that one of the vector patterns could not be compiled
and therefore cannot be searched.
3.
5' and 3' sequence matches are identical; inconclusive
indicates that the 5' and 3' patterns provided were identical, and
that they only match the sequence once. Thus the program cannot
determine which part of the sequence is vector and which is
insert.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
biosed Replace or delete sequence sections
codcopy Reads and writes a codon usage table
cutseq Removes a specified section from a sequence
degapseq Removes gap characters from sequences
descseq Alter the name or description of a sequence
entret Reads and writes (returns) flatfile entries
extractalign Extract regions from a sequence alignment
extractfeat Extract features from a sequence
extractseq Extract regions from a sequence
listor Write a list file of the logical OR of two sets of sequences
makenucseq Creates random nucleotide sequences
makeprotseq Creates random protein sequences
maskfeat Mask off features of a sequence
maskseq Mask off regions of a sequence
newseq Type in a short new sequence
noreturn Removes carriage return from ASCII files
notseq Exclude a set of sequences and write out the remaining ones
nthseq Writes one sequence from a multiple set of sequences
pasteseq Insert one sequence into another
revseq Reverse and complement a sequence
seqret Reads and writes (returns) sequences
seqretsplit Reads and writes (returns) sequences in individual files
skipseq Reads and writes (returns) sequences, skipping first few
splitter Split a sequence into (overlapping) smaller sequences
trimest Trim poly-A tails off EST sequences
trimseq Trim ambiguous bits off the ends of sequences
union Reads sequence fragments and builds one sequence
yank Reads a sequence range, appends the full USA to a list file
Author(s)
|
