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The extent of this non-specific hybridization can be reduced by blocking the repeat sequences by prehybridization with unlabeled genomic DNA see Figure 5. But this does not completely solve the problem, especially if the walk is being carried out with long inserts from high-capacity vectors such as BACs or YACs.
For this reason, intact inserts are rarely used for chromosome walks with human DNA and similar DNAs which have a high frequency of genome-wide repeats. Instead, a fragment from the end of an insert is used as the probe, there being less chance of a genome-wide repeat occurring in a short end-fragment compared with the insert as a whole.
If complete confidence is required then the end-fragment can be sequenced before use to ensure that no repetitive DNA is present. If the end-fragment has been sequenced then the walk can be speeded up by using PCR rather than hybridization to identify clones with overlapping inserts. Primers are designed from the sequence of the end-fragment and used in attempted PCRs with all the other clones in the library.
A clone that gives a PCR product of the correct size must contain an overlapping insert Figure 6. To speed the process up even more, rather than performing a PCR with each individual clone, groups of clones are mixed together in such a way that unambiguous identification of overlapping ones can still be made.
The method is illustrated in Figure 6. PCRs are carried out as follows: Figure 6. The two oligonucleotides anneal within the end region of insert number 1. They are used in PCRs with all the other clones in the library. Only clone 15 gives a PCR product, showing that the inserts in clones 1 and 15 overlap. In this example, a library of clones has to be screened by PCR.
In most cases, the more Samples of each clone in row A of the first microtiter tray are mixed together and a single PCR carried out. This is repeated for every row of every tray - 80 PCRs in all. Samples of each clone in column 1 of the first microtiter tray are mixed together and a single PCR carried out.
This is repeated for every column of every tray - PCRs in all. Clones from well A1 of each of the ten microtiter trays are mixed together and a single PCR carried out. This is repeated for every well - 96 PCRs in all. As explained in the legend to Figure 6. Ambiguities arise only if a substantial number of clones turn out to be positive. Newer more rapid methods for clone contig assembly Even when the screening step is carried out by the combinatorial PCR approach shown in Figure 6.
The procedure has been extremely valuable in positional cloning , where the objective is to walk from a mapped site to an interesting gene that is known to be no more than a few Mb distant. It has been less valuable for assembling clone contigs across entire genomes, especially with the complex genomes of higher eukaryotes. So what alternative methods are there? The main alternative is to use a clone fingerprinting technique. One or a combination of the following techniques is used Figure 6.
Restriction patterns can be generated by digesting clones with a variety of restriction enzymes and separating the products in an agarose gel.
If two clones contain overlapping inserts then their restriction fingerprints will have bands in common, as both will contain fragments derived from the overlap region. Repetitive DNA fingerprints can be prepared by blotting a set of restriction fragments and carrying out Southern hybridization Section 4. As for the restriction fingerprints, overlaps are identified by looking for two clones that have some hybridizing bands in common.
Because genome-wide repeat sequences are not evenly spaced in a genome, the sizes of the products obtained after repetitive DNA PCR can be used as a fingerprint in comparisons with other clones, in order to identify potential overlaps. STS content mapping is particularly useful because it can result in a clone contig that is anchored onto a physical map of STS locations. Presuming the STS is single copy in the genome, then all clones that give PCR products must contain overlapping inserts.
As with chromosome walking, efficient application of these fingerprinting techniques requires combinatorial screening of gridded clones, ideally with computerized methodology for analyzing the resulting data. Whole-genome shotgun sequencing The whole-genome shotgun approach was first proposed by Craig Venter and colleagues as a means of speeding up the acquisition of contiguous sequence data for large genomes such as the human genome and those of other eukaryotes Venter et al.
Experience with conventional shotgun sequencing Section 6. This implies that 70 million individual sequences, each bp or so in length, corresponding to a total of 35 Mb , would be sufficient if the random approach were taken with the human genome. Seventy million sequences is not an impossibility: in fact, with 75 automatic sequencers, each performing sequences per day, the task could be achieved in 3 years.
The big question was whether the 70 million sequences could be assembled correctly. If the conventional shotgun approach is used with such a large number of fragments, and no reference is made to a genome map, then the answer is certainly no. The huge amount of computer time needed to identify overlaps between the sequences, and the errors, or at best uncertainties, caused by the extensive repetitive DNA content of most eukaryotic genomes see Figure 5.
But with reference to a map, Venter argued, it should be possible to assemble the mini-sequences in the correct way. To minimize the amount of finishing that is needed, the whole-genome shotgun approach makes use of at least two clone libraries, prepared with different types of vector.
Two libraries are used because with any cloning vector it is anticipated that some fragments will not be cloned because of incompatibility problems that prevent vectors containing these fragments from being propagated.
Different types of vector suffer from different problems, so fragments that cannot be cloned in one vector can often be cloned if a second vector is used. Generating sequence from fragments cloned in two different vectors should therefore improve the overall coverage of the genome.
What about the problems that repeat elements pose for sequence assembly? We highlighted this issue in Chapter 5 as the main argument against the use of shotgun sequencing with eukaryotic genomes, because of the possibility that jumps between repeat units will lead to parts of a repetitive region being left out, or an incorrect connection being made between two separate pieces of the same or different chromosomes see Figure 5.
Several possible solutions to this problem have been proposed Weber and Myers, , but the most successful strategy is to ensure that one of the clone libraries contains fragments that are longer than the longest repeat sequences in the genome being studied.
For example, one of the plasmid libraries used when the shotgun approach was applied to the Drosophila genome contained inserts with an average size of 10 kb , because most Drosophila repeat sequences are 8 kb or fewer.
Sequence jumps, from one repeat sequence to another, are avoided by ensuring that the two end-sequences of each kb insert are at their appropriate positions in the master sequence Figure 6. In Figure 5. The result of such an more The initial result of sequence assembly is a series of scaffolds , each one comprising a set of sequence contigs separated by sequence gaps - ones which lie between the mini-sequences from the two ends of a single cloned fragment and so can be closed by further sequencing of that fragment Figure 6.
The scaffolds themselves are separated by physical gaps, which are more difficult to close because they represent sequences that are not in the clone libraries. The marker content of each scaffold is used to determine its position on the genome map.
For example, if the locations of STSs in the genome map are known then a scaffold can be positioned by determining which STSs it contains. If a scaffold contains STSs from two non-contiguous parts of the genome then an error has occurred during sequence assembly. The accuracy of sequence assembly can be further checked by obtaining end-sequences from fragments of kb or more that have been cloned in a high-capacity vector. If a pair of end-sequences do not fall within a single scaffold at their anticipated positions relative to each other, then again an error in assembly has occurred.
Two scaffolds are shown. Each comprises a series of sequence contigs separated by sequence gaps, with the scaffolds themselves separated by physical gaps. The feasibility of the whole-genome shotgun approach has been demonstrated by its application to the fruit-fly and human genomes Adams et al. The question that remains, and which has been hotly debated Patterson, , is whether the sequences obtained by the whole-genome shotgun approach have the desired degree of accuracy.
Part of the problem is that the random nature of sequence generation means that some parts of the genome are covered by several of the mini-sequences that are obtained, whereas other parts are represented just once or twice Figure 6. It is generally accepted that every part of a genome should be sequenced at least four times to ensure an acceptable level of accuracy, and that this coverage should be increased to 8—10 times before the sequence can be looked upon as being complete.
A sequence obtained by the whole-genome shotgun approach is likely to exceed this requirement in many regions, but may fall short in other areas. If those areas include genes, then the lack of accuracy could cause major problems when attempts are made to locate the genes and understand their functions see Chapter 7. These problems have been highlighted by studies of the Drosophila genome sequence, which have suggested that as many as of the 13 genes might contain significant sequence errors Karlin et al.
The random nature of sequence generation by the whole-genome shotgun approach means that some parts of the genome are covered by more mini-sequences than other parts. The Human Genome Projects To conclude our examination of mapping and sequencing we will look at how these techniques were applied to the human genome.
Although every genome project is different, with its own challenges and its own solutions to those challenges, the human projects illustrate the general issues that have had to be addressed in order to sequence a large eukaryotic genome, and in many ways illustrate the procedures that are currently regarded as state of the art in this area of molecular biology.
The mapping phase of the Human Genome Project Until the beginning of the s a detailed map of the human genome was considered to be an unattainable objective. Although comprehensive genetic maps had been constructed for fruit flies and a few other organisms, the problems inherent in analysis of human pedigrees Section 5.
The initial impetus for human genetic mapping came from the discovery of RFLPs, which were the first highly polymorphic DNA markers to be recognized in animal genomes. This map, developed from analysis of 21 families, had an average marker density of one per 10 Mb. In the late s the Human Genome Project became established as a loose but organized collaboration between geneticists in all parts of the world.
One of the goals that the Project set itself was a genetic map with a density of one marker per 1 Mb , although it was thought that a density of one per 2—5 Mb might be the realistic limit. In fact by an international consortium had met and indeed exceeded the objective, thanks to their use of SSLPs and the large CEPH collection of reference families Section 5.
The map contained markers, of which over were SSLPs, and had a density of one marker per 0. A subsequent version of the genetic map Dib et al. Physical mapping did not lag far behind.
In the early s considerable effort was put into the generation of clone contig maps, using STS screening Section 5. The major achievement of this phase of the physical mapping project was publication of a clone contig map of the entire genome, consisting of 33 YACs containing fragments with an average size of 0.
The use of these chimeric clones in the construction of contig maps could result in DNA segments that are widely separated in the genome being mistakenly mapped to adjacent positions. These problems led to the adoption of radiation hybrid mapping of STS markers Section 5. This map was later supplemented with an additional 20 STSs, most of these being ESTs and hence positioning protein-coding genes on the physical map Schuler et al.
The resulting map density approached the target of one marker per kb set as the objective for physical mapping at the outset of the Human Genome Project.
As a result, the physical and genetic maps could be directly compared, and clone contig maps that included STS data could be anchored onto both maps. The net result was a comprehensive, integrated map Bentley et al. Sequencing the human genome The original plan was that the sequencing phase of the Human Genome Project would be based on YAC libraries, because this type of vector can be used with DNA fragments longer than can be handled by any other type of cloning system.
This strategy had to be abandoned when it was discovered that some YAC clones contain non-contiguous fragments of DNA. At about the time when the Human Genome Project was gearing itself up to move into the sequence-acquisition phase, the whole-genome shotgun approach was first proposed as an alternative to the more laborious clone contig method that had so far been adopted Venter et al.
The possibility that the Human Genome Project would not in fact provide the first human genome sequence stimulated the organizers of the Project to bring forward their planned dates for completion of a working draft Collins et al. The first sequence of an entire human chromosome number 22 was published in December Dunham et al.
Finally, on 26 June , accompanied by the President of the United States, Francis Collins and Craig Venter, the leaders of the two projects, jointly announced completion of their working drafts Marshall, , which appeared in print eight months later IHGSC, ; Venter et al.
It is important to understand that the two genome sequences published in are drafts, not complete final sequences. This draft sequence comprises approximately 50 scaffolds see Figure 6. Similar statistics apply to the whole-genome shotgun sequence. Moving the Platform Beyond Dos.
Michael Rothman. Quick Boot.
Embedded Firmware Solutions: Development Best Practices for the Internet of Things. Vincent Zimmer. Windows Internals, Part 1: System architecture, processes, threads, memory management, and more 7th Edition. Pavel Yosifovich. Rootkits and Bootkits: Low-Level Programming: Igor Zhirkov.
Read more. Product details Paperback: Intel Press; 2nd edition Language: English ISBN Don't have a Kindle? Try the Kindle edition and experience these great reading features: Share your thoughts with other customers. Write a customer review. Top Reviews Most recent Top Reviews. There was a problem filtering reviews right now.
Please try again later. Paperback Verified download. This book does not provide anything close to a tutorial, and the tutorials available on the Tianocore GitHub seem to be out of date. For instance, when building UEFI using the tutorials, I ran into several warnings, and even errors when building: I was hoping this text would help feel in gaps, but not even close.
Handy as a reference. But this is not a how-to or hand-holding introduction. You wont find a step-by-step guide to beginning EFI development. That said, after reading the book, I've been able to jump right into development of simple EFI applications. And I'm loving it! I would certainly recommend the book, but then again you're selection as far as EFI is concerned, is rather Based on the title, I was expecting a book whose focus would be developing drivers and other interfaces to system UEFI software.
Instead, the focus of the book seems to be largely a history and architectural overview of the EFI and UEFI standards and interfaces development, which is interesting to some software engineers, but not terribly useful to people hoping to interface to UEFI software. As expected. I am a UEFI veteran. While the information inside this book is useful as a reference, it is terribly written.
Many many times terms and abbreviations are used without definition before they are used. Diagrams are simplistic and many could be simple point-form short lists. Cross references to figures in text that don't exist. Sentences that obviously have never been looked at by an editor and make no sense. Sections that mention a protocol but never define or explain it. Change of names of terms midway through a set of diagrams with no explanation. It is clear that there were three authors and that for the most part they never talked to each other about the content of their chapters, because of the massive amount of duplication and innacurate assumptions made about content made elsewhere.
Use this as a reference if you know stuff about UEFI, but learning from scratch with it is going to be pretty hard.