Sequence databases

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  • Many applications require the use of unique numbers as primary key values. You can either build code into the application to handle this requirement or use a sequence to generate unique numbers. This lesson covers creating and using sequences that create unique numbers. At the end of this lesson, you should be able to  Explain the use of sequences.  Create a sequence.  Use a sequence.  Modify a sequence definition.  Remove a sequence.

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  • Protein family databases obtain sequences fromone of the large protein sequence databases,most commonly SWISS- PROT with TrEMBL (Bairoch and Apweiler, 2000) but also PIR (Barker et al., 2000). They then apply an algorithm, either manual or automatic, to group the sequences into families. Each family is represented in one or more ways to facilitate both inspection by humans and comparison by computer programs. The most common representation is a multiple alignment of the family’s sequences, either with insertion and deletion (gap) characters or without.

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  • [ Team LiB ] Recipe 4.4 Getting a Sequence Value from Oracle Problem When you add a row into an Oracle table that uses a sequence to generate the value for a primary key column, the value assigned to the column in the DataTable is replaced by a value generated by the database.

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  • Several efforts have been made since 1990 to overcome the effort required to maintain curated protein family data- bases by automatically clustering the protein sequence databases using sequence similarity. The general approach is to compute all possible pairwise comparisons, and then cluster them in some fashion, shifting the effort from humans to computers. This otherwise computationally very demanding process has benefited from the introduc- tion of the rapid PSI-BLAST system(Altschul et al., 1997).

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  • ProDom(Corpet et al., 2000) is one of the earliest clustered protein family databases and continually updates its methods and services. Currently, it coordinates some of its larger entries with Pfam-A and uses PSI-BLAST to cluster the remaining sequences in SWISS-PROT and TrEMBL. While only large entries have been scrutinized manually, the consistency of all families is assessed by computing a series of numerical measurements. The resulting families are represented as consensus sequences and gapped multiple alignments.

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  • A sequence: Automatically generates unique numbers Is a sharable object Is typically used to create a primary key value Replaces application code Speeds up the efficiency of accessing sequence values when cached in memory

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  • Before you begin this course, you should be able to use a graphical user interface (GUI). Required prerequisites are familiarity with data processing concepts and techniques.  Introduction to Oracle: SQL and PL/SQL Using Procedure Builder is an instructor-led course featuring lecture and hands-on exercises. The concepts and skills introduced are reinforced by online demonstrations and written practice sessions.

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  • Partitioning DFDs: a. The process of analyzing a DFD and deriving a series of manual procedures b. Adding controls to ensure the processes are done property c. The process of analyzing a DFD and deriving a series manual procedures and computer programs d. None of these answers Câu 162: Physical data flow diagram: a. describing processes in greater detail b. show sequencing processes in the order they must be executed c. show how the system operates or how the new system will be implemented d. all of these answers Câu 163: Physical DFDs a. show how the system is or...

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  • For simplicity, in the example we have assumed that a new map is created at the end of every step. This is certainly a possibility, but it is not necessarily the best option. Later in this book, we will discuss data modeling and how to optimize the sequence of operations. In particular, Chapters 8 and 9 cover spatial operators and functions that make it possible to cluster some of the steps in the example into single queries, making the process much simpler and more efficient.

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  • A major stumbling block of manual approaches is the problem of keeping the alignments up to date with new releases of protein sequences.Arobust and efficient updating scheme is required to ensure stabil- ity of the database. These requirements are met in Pfam by using two alignments: a high quality seed alignment, which changes only little or not at all between releases, and a full alignment, which is built by automatically aligning all members to a hidden Markov model-based profile (HMM) derived from the seed alignment.

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  • Despite its importance in plant metabolism, no sequences of higher plant ATP-dependent phosphofructokinase (EC 2.7.1.11) are annotated in the databases. We have purified the enzyme from spinach leaves 309-fold to electrophoretic homogeneity. The purified enzyme was a homotetramer of 52 kDa subunits with a specific activity of 600 mUÆmg )1 and aKmvalue for ATP of 81 lm.

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  • The Internet is a loosely coupled federation of computer servers and clients. Clients are sometime disconnected, and yet they need to be able continue functioning. Rather than building tightly- coupled RPC-based applications, Internet-scale applications must be constructed as asynchronous tasks structured as workflows involving multiple autonomous agents. eMail gives an intuitive understanding of these design issues. You want to be able to read and send mail...

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  • Data is increasingly generated by instruments that monitor the environment – telescopes looking at the heavens, DNA sequenc- ers decoding molecules, bar-code readers watching passing freight-cars, patient monitors watching the life-signs of a person in the emergency room, cell-phone and credit-card systems look- ing for fraud, RFID scanners watching products flow through the supply chain, and smart-dust sensing its environment. In each of these cases, one wants to compare...

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  • The database community has insulated itself from the information retrieval community, and has largely eschewed dealing with messy data types like time and space (not everyone has, just most of us.) We had our hands full dealing with the “simple stuff” of numbers, strings, and relational operators on them. But, real ap- plications have massive amounts of text data, have temporal prop- erties, and have spatial properties. The DBMS extensibility offered by integrating languages with the DBMS makes it relatively easy to add data types...

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  • The code executed by the replica proxy for supporting Byzantine clients is presented in Figure 4. To be able to compare if the sequence of operations submitted initially is the same that is submitted at commit time, the coor- dinator also logs the operations and their results as they are executed (line 42). At commit time, if the received list differs from the log, the coordinator discards exe- cuted operations in the current transaction and executes operations in the received list, as any other replica.

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  • The state of a normal or diseased cell is determined by external signals and by its intrinsic gene expression pat- tern. Transcription factors (TFs) are major regulators of gene expression, typically controlling more than one gene and acting in concert. Such TF-gene interactions can be described as networks, which are crucial to understand hierarchies of gene expression regulation. The identifica- tion of TF binding sites (TFBSs) in genomic DNA sequences has played an important role in predicting tran- scriptional networks.

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  • The prediction of transcription factor binding sites in genomic sequences is in principle very useful to identify upstream regulatory factors. However, when applying this concept to genomes of multi- cellular organisms such as mammals, one has to deal with a large number of false positive predic- tions since many transcription factor genes are only expressed in specific tissues or cell types.

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  • As detection of relationships improves with more samples and better methodology, families and super- families can become more populated. At present, structur- al relationships provide the highest level of classification, and structure-based databases classify proteins with similar ‘folds’. These classifications reveal that whenever structures are known for two proteins that are considered members of the same family or superfamily, the structures are similar, whereas the converse is often not true.

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  • We choose the kinesins to illustrate similarities and differences between protein family databases. Kinesin and its relatives are motor proteins that utilize ATP hydrolysis to move along microtubules in eukaryotic cells. The motor portion of a kinesin is structurally very similar to that of the myosin motor, which moves along actin filaments, although no sequence similarity is evident between them. This is an example of likely divergence from an ancestral fold that is beyond current sequence- based comparison methods to detect.

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  • Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành y học dành cho các bạn tham khảo đề tài: GarlicESTdb: an online database and mining tool for garlic EST sequences

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