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Topic: Sequence profiling tool

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	Bioinformatics - Wikipedia, the free encyclopedia
		HT studies are often used to determine the genes implicated in a disorder: one might compare microarray data from cancerous epithelial cells to data from non-cancerous cells to determine the proteins that cancer up-regulates and down-regulates.
		In the genomic branch of bioinformatics, homology is used to predict the function of a gene: if the sequence of gene A, whose function is known, is homologous to the sequence of gene B, whose function is unknown, one could infer that B may share A's function.
		DNA sequences of endangered species can be preserved, and names and descriptions of specimens living in captivity are stored in order to allow as much access to the information needed to preserve biodiversity as possible.
	en.wikipedia.org /wiki/Bioinformatics (2062 words)

	Sequerome (Site not responding. Last check: 2007-11-03)
		This tool provides a unique and useful functionality of profiling each of the BLAST results to enable the users to extract the maximum out sequence alignment reports.
		Another distinctive feature of this tool is the simultaneous tracking of all your analysis and manipulations as 'icons' in a nearby panel.
		Moreover, it is difficult to navigate smoothly between different sequence alignment records.
	bioinformatics.georgetown.edu /Sequerome.htm (318 words)

	Bioinformatics - Encyclopedia.WorldSearch (Site not responding. Last check: 2007-11-03)
		Major research efforts in the field include sequence alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution.
		Evolutionary biology is the study of the origin and descent of species, as well as their change over time.
		Further analysis could take a variety of directions: one 2004 study analyzed the promoter sequences of co-expressed (clustered together) genes to find common regulatory elements and used machine learning techniques to predict the promoters involved in regulating each cluster (see this study).
	encyclopedia.worldsearch.com /bioinformatics.htm (1523 words)

	Performance Profiler Description
		The profiler server also dynamically creates and deletes the memory regions that are used to construct the call graph and count the profiling ticks (see the following section).
		While the performance profiler is active, the system is regularly interrupted by the profiling clock (which by default is the system clock).
		The accuracy of the reported percentage of time spent is about five percent when the number of profiling ticks is in the order of magnitude of ten times the number of bytes in the profiled programs.
	www.jaluna.com /doc/c5/html/AppliDevGuide/x6829.html (536 words)

	The Java Virtual Machine Profiler Interface (JVMPI)
		If the defining events are not enabled, the profiler agent may receive an unknown ID. In that case the profiler agent may request the corresponding defining event to be sent on demand by issuing a RequestEvent call.
		It is not safe for the profiler agent to call this function in the thread suspended mode because the current thread may block on the raw monitor already acquired by one of the suspended threads.
		The profiler must allocate the space for the modified class file data buffer using the memory allocation function pointer sent in this event, because the VM is responsible for freeing the new class file data buffer.
	java.sun.com /j2se/1.4.1/docs/guide/jvmpi/jvmpi.html (6246 words)

	DNA array systems
		High throughput expression profiling had been initially designed to provide a means of assigning function to genes at the same pace as sequencing projects released data.
		If in a time course experiment, assayed by microarray, several genes can be clustered together, the ones for which sequence data were the only experimental evidence of their existence can then be assigned to a biological process by virtue of being co-regulated with genes of known functions.
		In other words, any given expression profiling experiment delivers data that can potentially be mined to annotate genes, provide insight about which genes are involved in the inception of a biological event, and finally describe complex biological systems at the molecular level.
	www.dnaarray.com /news/onto-express_news.html (828 words)

	[No title] (Site not responding. Last check: 2007-11-03)
		In response to the stimulation mediated by a wide variety of materials and signals, after they are incorporated into cells, a number of genes respond in a number of ways specific to the types of the stimulation, materials and cells.
		Therefore, the cellular responses to hormones and the effects of such responses can be monitored by examining or profiling the responses by the genes, which is essential for the application of hormone-based assays.
		In the second field, gene expression profiling of environmental hormones, or endocrine disruptors, will be a useful tool for monitoring effects of industrial chemicals, and natural and artificial biomaterials.
	research.haifa.ac.il /~genom/Conference/Abstracts/2nd_3rd/Kiyama.doc (399 words)

	The Detailed Structure of a Model Breast Cancer Genome
		This technology is unique in that it uses the normal, non-cancerous sequence of the human genome as a "baseline ruler" to determine the structural organization of a tumor genome.
		End Sequence Profiling (ESP) is a sequence-based approach capable of precisely identifying, characterizing and cloning en masse structural rearrangements and variations in a tumor genome at very high resolution.
		BAC sequences at either end of the cloned DNA are then generated for individual BAC clones and mapped onto the normal “reference” genome sequence.
	www.cbcrp.org /research/PageGrantPrintPage.asp?grant_id=2330 (1247 words)

	ONJava.com: Performance Analysis of J2EE Applications Using AOP Techniques
		We describe the architecture of the profiling tool and then the advices that were developed to instrument the application.
		Since all of the profiling information is in a database, we can write different kinds of SQL queries to view the profiling data from different angles.
		The first advice is used to capture the sequence of method execution, the second one captures the performance metrics of Java method execution, and the third one captures the SQL execution times.
	www.onjava.com /pub/a/onjava/2004/05/12/aop.html (958 words)

	[No title]
		The profile is based upon the procedure call graph and allows the user to answer questions of the form "How much time is spent in the procedure printf() and all its descendents?".
		If the tools cannot determine the correct parameters for the machine you are running on, an error message will be printed and the default will be to simulate the application running on the DEC 3000 Model 500.
		These operations must be accomplished with a sequence of instructions that read a longword (32 bits) or quadword(64 bits), extract the corresponding data, modify it, replace the corresponding data inside of the quadword, and write the new value to memory.
	www.cs.cmu.edu /afs/cs.cmu.edu/academic/class/15213-f98/atom/man5/atomtools.5 (4174 words)

	CrimTrac - DNA (Site not responding. Last check: 2007-11-03)
		DNA profiling is the single most important advance in police investigation techniques since the development of fingerprint classification systems in the late nineteenth century.
		DNA profiles are a very powerful means of determining whether two samples may or may not have come from the same person.
		Profiles will be removed from the database in accordance with destruction dates notified by the jurisdictions.
	www.crimtrac.gov.au /dna.htm (1044 words)

	OpinionJournal - DE GUSTIBUS
		By this I don't mean that we must be less tolerant of others but that some among us must learn to tolerate--or put up with--hardships, inconvenience or a new set of presumptions, given the all-consuming nature of the threat we face, in which "the profiled" and "the profilers" alike are targets.
		Here, one must be satisfied either that profiling ought to be done or at least--per Bentham--that it isn't something that "ought not to be done." I am satisfied on the second count.
		The profiling process is not precisely racial but broadly physical according to "Muslim type." (Does that make it worse or better?) The process under way now does not constitute racial profiling in the classic sense--Muslims, after all, come in flavors other than Pakistani, including white Chechens and fl Somalis.
	www.opinionjournal.com /forms/printThis.html?id=110007032 (717 words)

	KcacheGrindGlossary (Site not responding. Last check: 2007-11-03)
		Profile Data File: A file containing data measured in a profile experiment (or part of) or produced by postprocessing a trace.
		Profile Experiment: A program run supervised by a profiling tool, producing possibly multiple profile data files from parts and/or threads of the run.
		Profile Project: A configuration for profile experiments used for one program which has to be profiled, perhaps in multiple versions.
	kcachegrind.sourceforge.net /cgi-bin/show.cgi/KcacheGrindGlossary (352 words)

	POULTRY RESEARCH IN THE POST-GENOME ERA (Site not responding. Last check: 2007-11-03)
		The genome sequence should facilitate studies of functional genomics that aim to identify genes and their regulatory elements, the encoded gene products and the gene expression patterns for various metabolic processes.
		With a complete genome sequence, the search for candidate genes that are in close proximity to a marker linked to a desirable trait is greatly simplified.
		For example, the approach being used by Hans H. Cheng (hcheng@msu.edu) to dissect the molecular basis for Marek's disease virus infection involves the mapping of candidate genes by QTL analysis, categorizing differential gene expression by microarray analysis, and examining protein-protein interactions using a yeast two-hybrid screen.
	www.nbiap.vt.edu /articles/feb0405.htm (728 words)

	The Harvard Atom-like Tool (Halt) Manual
		Halt was initially designed as a profiling tool, so unsurprisingly there are a number of pieces of code that support tracing and profiling that are part of the distribution.
		The training profile is used by profile-driven layout decisions; the testing profile is used to calculate how well the layout decisions work on a different run of the program.
		Many instruction schedulers use profiles to direct their attention to frequently executed portions of the program, where it is worth paying in terms of program size and optimization time to make the final program run faster.
	www.eecs.harvard.edu /hube/software/v112/halt2.html (6827 words)

	Profile
		"Sequence Profiling Tools": In bioinformatics, this refers to all those software tools (web-based/downloadable) that provide a brief overview on all related information about an input sequence.
		The advent of post-genomics era has given rise to a range of web based tools and software to handle the deluge of biological information.
		Natarajan Ganesan, Nicholas F. Bennett, Mahendran Velauthapillai, Nagarajan Pattabiraman, Richard Squier, and Bala Kalyanasundaram,SEQUEROME: A 'Sequence Profiling Tool' for genome and Proteome analysis.
	myprofile.cos.com /natarajang (1025 words)

	PP: A Path Profiling Tool (Site not responding. Last check: 2007-11-03)
		For example, the events can be simply the beginnings of new paths, in which case the profile just counts the number of times each path executes, or the events can be hardware events like data cache misses, in which case the profile counts the number of times each path suffered a cache miss.
		In context profiling, the paths are paths in the call graph: events are associated with nodes in a data structure called the calling context tree, which is a bounded representation of the dynamic call tree.
		The algorithms in PP are described in: Thomas Ball and James Larus, Efficient Path Profiling, MICRO-29, December 1996.
	www.cs.wisc.edu /~larus/pp.html (537 words)

	Research (Site not responding. Last check: 2007-11-03)
		One important tool for understanding the relationship between the structure of these building blocks and the functions they encode is site-directed mutagenesis, in which a specific amino acid in a protein can be replaced with any of the other nineteen common amino acids.
		The most efficient 4-base codon suppressors had Watson-Crick complementary anticodons, and the sequences of the anticodon loops outside of the anticodons varied with the anticodon.
		However, N-length codons were found to prefer N + 4 length anticodon loops, and sequence preferences in the loops were evident, including the requirement of Watson-Crick complementarity to the codon.
	schultz.scripps.edu /Research/UnnaturalAAIncorporation/research.html (3475 words)

	Tool Report: HPjmeter
		We repeated the sequence of actions that we knew was leaving behind objects on the heap, and closed the application.
		The last column shows the "bytes held." This is the total number of bytes that could be de-allocated from the heap by the garbage collector, if the particular object "died" (that is, if all references to this object were nullified).
		Naturally, the tool is unable to tell if the object is kept alive intentionally or not.
	www.javaperformancetuning.com /tools/hpjmeter/index.shtml (2387 words)

	VOTE: Visual Object Tracing Engine (Site not responding. Last check: 2007-11-03)
		Some profiling and tracing tools such as DEC’s PIXIE and QPT from University of Wisconsin are available only on the UNIX platform.
		A similar tool has been developed in Finland in University of Helsinky: more information about it can be found at http://www.cs.helsinki.fi/~viljamaa/kana/kanahelp.html#kappale12.
		With systems that are heavily timer driven, the profile of the Autologged system can be expected to differ in the ordering of events from that of the non-monitored system.
	www.cs.cornell.edu /carrer/vote/VOTE.html (1579 words)

	New DSP Tool Lets You See More
		So next time your application breaks on an error condition you will be able to examine the last 256K cycles of the executed code and find the sequence of events that lead to the error.
		All interrupt activity is shown in the actual sequence of occurrence along with the time of the interrupt, duration and repetition rate.
		Once the application code is finished the Code Profiler Window will be used to provide you with the necessary tools to capture and display the application execution profile.
	www.signum.com /DSPTrace.htm (552 words)

	B.U. Bridge: Boston University community's weekly newspaper
		Now that the race to sequence the human genome has produced a virtual tie at the finish line, the challenge is to identify the useful information within the billions of sequences now stored in the huge public and private databases maintained by the National Center for Biotechnology Information and others.
		These tools and algorithms significantly reduce the time and cost involved in identifying useful genetics and expression information.
		It also led to a provisional patent on the bioinformatics tool, and negotiations are now under way for the commercialization of this technique.
	www.bu.edu /phpbin/researchbriefs/display.php?id=348 (424 words)

	Tool Report: JProbe
		We profile the application again while performing the use case to request a stock chart for several different stocks and we capture another snapshot of our application?s performance data.
		JProbe Profiler?s snapshot differencing feature will allow us to determine exactly what the performance difference is. As we load the two snapshots and take the difference, we see that we made a 98.7% improvement gain (4,466 ms) in the Method Time for the assignData method (see Figure 14).
		The JProbe Suite of tools with its developer-oriented features like filtering, visual indicators to various problems, detailed performance and memory metrics, source code browsing, and snapshot differencing helps even seasoned Java developers to quickly resolve performance and memory issues in their applications.
	www.javaperformancetuning.com /tools/jprobe/index.shtml (4109 words)

	Profile (Site not responding. Last check: 2007-11-03)
		Combined with SPINDLE~SENSE, controls where material is relative to the tool during a profiling milling NC sequence.
		This allows the tool to follow surfaces defined by the part, a datum, or by sketching.
		Usually a long milling tool is used, and it follows the surface defined and therefore removes excess stock
	www.staffs.ac.uk /~entdgc/ProeTutor/machining/Glossary.html (368 words)

	COGBURN ET AL., June 2003
		DNA sequence clustering was used to build contigs of overlapping sequence and to identify unique, non-redundant EST clones (unigenes), which permitted printing of systems-wide chicken DNA microarrays.
		We are using DNA microarrays for global gene expression profiling to identify candidate genes and to map growth, metabolic, and regulatory pathways that control important production traits.
		Thus, genome-wide transcriptional profiling is a powerful tool used to visualize the cascade of genetic circuits that govern complex biological responses.
	www.poultryscience.org /ps/abs/03/p0360939.htm (390 words)

	Canadian Bioinformatics Help Desk Newsletter -- December 16, 2004 (Site not responding. Last check: 2007-11-03)
		This web server is designed to display sequence alignment results so that more information can be gleaned from each of the 'hits' in a BLAST search report without having to leave the browser session.
		Present a 'Nucleotide sequence to Protein structure' interface to a user who has little or no idea of the possible structural or functional domains contained within his or her ORF.
		This workshop is the foundation for a Certificate in Bioinformatics accredited by the Universities of Toronto, New Brunswick and British Columbia and recognized by the American Medical Association and the Royal College of Physicians and Surgeons.
	www.gchelpdesk.ualberta.ca /news/16dec04/cbhd_news_16dec04.php (3257 words)

	AntiOffline We really DO give a flying f##k (Site not responding. Last check: 2007-11-03)
		The command sequence to turn them off is: *CONFIG (on newer routers) or TALK 6 (on older routers) Config>PROTOCOL IP IP Config>DISABLE DIRECTED-BROADCAST A restart of the router is then required.
		An # attacker may use the time information to schedule an attack at a # period of time when the system may run a cron job (or other time- # based event) or otherwise be busy.
		It may also be possible predict # ID or sequence numbers that are based on the time of day for spoofing # services.
	www.antioffline.com /stoppingdos.html (2331 words)

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