232:(BAC) library screened has low complexity, meaning it does not contain a high number of STS or restriction sites, or if certain regions were less stable in cloning hosts and thus underrepresented in the library. If gaps between contigs remain after STS landmark mapping and restriction fingerprinting have been performed, the sequencing of contig ends can be used to close these gaps. This end-sequencing strategy essentially creates a novel STS with which to screen the other contigs. Alternatively, the end sequence of a contig can be used as a primer to
196:. Since these clones should cover the entire genome/chromosome, it is theoretically possible to assemble a contig of BACs that covers the entire chromosome. Reality, however, is not always ideal. Gaps often remain, and a scaffold—consisting of contigs and gaps—that covers the map region is often the first result. The gaps between contigs can be closed by various methods outlined below.
220:. If two clones, they will likely have restriction sites in common, and will thus share several fragments. Because the number of fragments in common and the length of these fragments is known (the length is judged by comparison to a size standard), the degree of overlap can be deduced to a high degree of precision.
181:
the minimum number of clones that form a contig that covers the entire chromosome comprise the tiling path that is used for sequencing. Once a tiling path has been selected, its component BACs are sheared into smaller fragments and sequenced. Contigs therefore provide the framework for hierarchical sequencing.
208:(STS) content mapping to detect unique DNA sites in common between BACs. The degree of overlap is roughly estimated by the number of STS markers in common between two clones, with more markers in common signifying a greater overlap. Because this strategy provides only a very rough estimate of overlap,
108:
then searches this database for pairs of overlapping reads. Assembling the reads from such a pair (including, of course, only one copy of the identical sequence) produces a longer contiguous read (contig) of sequenced DNA. By repeating this process many times, at first with the initial short pairs of
180:
is made prior to sequencing in order to provide a framework to guide the later assembly of the sequence reads of the genome. This map identifies the relative positions and overlap of the clones used for sequencing. Sets of overlapping clones that form a contiguous stretch of DNA are called contigs;
128:
longer DNA fragments are sequenced. Here, a contig still refers to any contiguous stretch of sequence data created by read overlap. Because the fragments are of known length, the distance between the two end reads from each fragment is known. This gives additional information about the orientation
76:
In order to make it easier to talk about our data gained by the shotgun method of sequencing we have invented the word "contig". A contig is a set of gel readings that are related to one another by overlap of their sequences. All gel readings belong to one and only one contig, and each contig
98:
strategy involves shearing genomic DNA into many small fragments ("bottom"), sequencing these fragments, reassembling them back into contigs and eventually the entire genome ("up"). Because current technology allows for the direct sequencing of only relatively short DNA fragments (300–1000
140:
Scaffolds consist of overlapping contigs separated by gaps of known length. The new constraints placed on the orientation of the contigs allows for the placement of highly repeated sequences in the genome. If one end read has a repetitive sequence, as long as its
113:
145:
is located within a contig, its placement is known. The remaining gaps between the contigs in the scaffolds can then be sequenced by a variety of methods, including PCR amplification followed by sequencing (for smaller gaps) and
103:
DNA is sheared randomly into fragments appropriately sized for sequencing. The subsequent sequence reads, which are the data that contain the sequences of the small fragments, are put into a database. The
77:
contains at least one gel reading. The gel readings in a contig can be summed to form a contiguous consensus sequence and the length of this sequence is the length of the contig.
66:. Contigs can thus refer both to overlapping DNA sequences and to overlapping physical segments (fragments) contained in clones depending on the context.
109:
reads but then using increasingly longer pairs that are the result of previous assembly, the DNA sequence of an entire chromosome can be determined.
212:
fragment analysis, which provides a more precise measurement of clone overlap, is often used. In this strategy, clones are treated with one or two
304:
86:
A sequence contig is a continuous (not contiguous) sequence resulting from the reassembly of the small DNA fragments generated by
189:
184:
The assembly of a contig map involves several steps. First, DNA is sheared into larger (50–200kb) pieces, which are cloned into
28:
229:
185:
159:
147:
204:
BAC contigs are constructed by aligning BAC regions of known overlap via a variety of methods. One common strategy is to use
134:
99:
nucleotides), genomic DNA must be fragmented into small pieces prior to sequencing. In bottom-up sequencing projects,
534:
100:
116:
Overlapping reads from paired-end sequencing form contigs; contigs and gaps of known length form scaffolds.
121:
205:
217:
91:
213:
209:
172:
87:
55:
47:
43:
465:"Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses"
539:
494:
426:
377:
300:
193:
63:
484:
476:
416:
408:
367:
359:
329:
489:
464:
245:
233:
105:
95:
51:
421:
396:
372:
347:
528:
177:
163:
112:
59:
228:
Gaps often remain after initial BAC contig construction. These gaps occur if the
90:
strategies. This meaning of contig is consistent with the original definition by
16:
Set of overlapping DNA segments that together represent a consensus region of DNA
348:"A new computer method for the storage and manipulation of DNA gel reading data"
514:
363:
333:
142:
520:
Staden package of sequence assembly: Definitions and background information
498:
412:
129:
of contigs constructed from these reads and allows for their assembly into
480:
381:
176:
sequencing strategy is used. In this sequencing method, a low-resolution
430:
111:
519:
42:) is a set of overlapping DNA segments that together represent a
58:
projects, contig refers to the overlapping clones that form a
397:"A strategy of DNA sequencing employing computer programs"
150:
cloning methods followed by sequencing for larger gaps.
50:
projects, a contig refers to overlapping sequence data (
442:
440:
62:of the genome that is used to guide sequencing and
515:Definition of the term and historical perspective
268:
266:
264:
262:
260:
463:Fullwood MJ, Wei C, Liu ET, et al. (2009).
299:(3rd ed.). Sinauer Associates. p. 84.
8:
320:
318:
316:
290:
288:
286:
284:
282:
488:
420:
371:
216:and the resulting fragments separated by
158:Contig can also refer to the overlapping
328:. Encyclopedia of Life Sciences, 2005.
295:Gibson, Greg; Muse, Spencer V. (2009).
276:. Encyclopedia of Life Sciences, 2005.
256:
450:. Encyclopedia of Life Sciences, 2005.
458:
456:
7:
14:
29:Contig (defragmentation utility)
230:Bacterial Artificial Chromosome
124:technology where both ends of
1:
70:Original definition of contig
27:defragmentation program, see
200:Construction of BAC contigs
120:Today, it is common to use
23:in DNA sequencing. For the
556:
297:A Primer of Genome Science
18:
166:of a chromosome when the
74:In 1980, Staden wrote:
334:10.1038/npg.els.0005353
44:consensus region of DNA
401:Nucleic Acids Research
352:Nucleic Acids Research
117:
94:(1979). The bottom-up
19:This article is about
481:10.1101/gr.074906.107
364:10.1093/nar/8.16.3673
122:paired-end sequencing
115:
413:10.1093/nar/6.7.2601
224:Gaps between contigs
206:sequence-tagged site
133:in a process called
88:bottom-up sequencing
48:bottom-up sequencing
218:gel electrophoresis
214:restriction enzymes
56:top-down sequencing
346:Staden, R (1980).
210:restriction digest
126:consistently sized
118:
535:Molecular biology
448:Genome Sequencing
395:Staden R (1979).
358:(16): 3673–3694.
306:978-0-878-93236-8
106:assembly software
547:
503:
502:
492:
460:
451:
444:
435:
434:
424:
407:(7): 2601–2610.
392:
386:
385:
375:
343:
337:
322:
311:
310:
292:
277:
270:
236:across the gap.
82:Sequence contigs
555:
554:
550:
549:
548:
546:
545:
544:
525:
524:
511:
506:
469:Genome Research
462:
461:
454:
445:
438:
394:
393:
389:
345:
344:
340:
323:
314:
307:
294:
293:
280:
274:Contig Assembly
271:
258:
254:
242:
226:
202:
156:
84:
72:
32:
17:
12:
11:
5:
553:
551:
543:
542:
537:
527:
526:
523:
522:
517:
510:
509:External links
507:
505:
504:
475:(4): 521–532.
452:
436:
387:
338:
326:Genome Mapping
312:
305:
278:
255:
253:
250:
249:
248:
246:Staden Package
241:
238:
225:
222:
201:
198:
192:to form a BAC
155:
152:
96:DNA sequencing
83:
80:
71:
68:
15:
13:
10:
9:
6:
4:
3:
2:
552:
541:
538:
536:
533:
532:
530:
521:
518:
516:
513:
512:
508:
500:
496:
491:
486:
482:
478:
474:
470:
466:
459:
457:
453:
449:
443:
441:
437:
432:
428:
423:
418:
414:
410:
406:
402:
398:
391:
388:
383:
379:
374:
369:
365:
361:
357:
353:
349:
342:
339:
335:
331:
327:
324:Dear, P. H.
321:
319:
317:
313:
308:
302:
298:
291:
289:
287:
285:
283:
279:
275:
269:
267:
265:
263:
261:
257:
251:
247:
244:
243:
239:
237:
235:
231:
223:
221:
219:
215:
211:
207:
199:
197:
195:
191:
187:
182:
179:
175:
174:
169:
165:
161:
153:
151:
149:
144:
138:
136:
132:
127:
123:
114:
110:
107:
102:
97:
93:
92:Rodger Staden
89:
81:
79:
78:
69:
67:
65:
61:
57:
53:
49:
45:
41:
37:
30:
26:
22:
472:
468:
447:
446:Dunham, I.
404:
400:
390:
355:
351:
341:
325:
296:
273:
272:Gregory, S.
227:
203:
183:
173:hierarchical
171:
167:
164:physical map
162:that form a
157:
139:
130:
125:
119:
85:
75:
73:
60:physical map
39:
35:
33:
24:
20:
234:primer walk
154:BAC contigs
135:scaffolding
529:Categories
252:References
40:contiguous
143:mate pair
131:scaffolds
101:amplified
540:Genomics
499:19339662
240:See also
168:top-down
64:assembly
490:3807531
382:7433103
194:library
497:
487:
431:461197
429:
422:327874
419:
380:
373:324183
370:
303:
160:clones
54:); in
38:(from
36:contig
25:contig
21:contig
52:reads
46:. In
495:PMID
427:PMID
378:PMID
301:ISBN
190:PACs
186:BACs
485:PMC
477:doi
417:PMC
409:doi
368:PMC
360:doi
330:doi
188:or
178:map
170:or
148:BAC
531::
493:.
483:.
473:19
471:.
467:.
455:^
439:^
425:.
415:.
403:.
399:.
376:.
366:.
354:.
350:.
315:^
281:^
259:^
137:.
34:A
501:.
479::
433:.
411::
405:6
384:.
362::
356:8
336:.
332::
309:.
31:.
Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
