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Topic: Genetic sequence

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	Sequence database -- Facts, Info, and Encyclopedia article (Site not responding. Last check: 2007-10-09)
		A database can include sequences from only one organism, as in databases including all the proteins in (Used as a leaven in baking and brewing) Saccharomyces cerevisiae, or it can include sequences from all organisms whose DNA has been sequenced.
		A major problem with all the large genetic sequence databases is that records are deposited in them from a wide range of sources, from individual researchers to large genome sequencing centers.
		Therefore, one must always regard the biological annotations in major sequence databases with a considerable degree of skepticism, unless they can be verified by reference to published papers describing high-quality experimental data, or at least by reference to a human-curated sequence database.
	www.absoluteastronomy.com /encyclopedia/s/se/sequence_database.htm (297 words)

	Genome Glossary
		Alternative form of a genetic locus; a single allele for each locus is inherited from each parent (e.g., at a locus for eye color the allele might result in blue or brown eyes).
		The gene sequence for the segment is reversed with respect to the rest of the chromosome.
		A method for amplifying a DNA base sequence using a heat-stable polymerase and two 20-base primers, one complementary to the (+) strand at one end of the sequence to be amplified and one complementary to the (-) strand at the other end.
	www.ornl.gov /sci/techresources/Human_Genome/glossary/glossary.shtml (6587 words)

	[No title]
		When the genetic program is executed, an array of the most recent mouse positions is passed in as input, which the program is free to use however it likes.
		In designing the language of the genetic code and the virtual machine for interpreting it, inspiration was taken from assembly languages and their use of low level instructions, an instruction pointer, and registers for storing data.
		However, genetic programs can be generated that contain infinite loops, dead code, code that has no effect on the output, or that generate output that is not a function of the mouse input.
	www.dgp.toronto.edu /~mjmcguff/csc2521/project/report (3644 words)

	GenBank Overview
		GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI.
		Many journals require submission of sequence information to a database prior to publication so that an accession number may appear in the paper.
		There are specialized, streamlined procedures for batch submissions of sequences, such as EST, STS, and HTG sequences.
	www.ncbi.nlm.nih.gov /Genbank/GenbankOverview.html (405 words)

	Mapping Factsheet
		In humans, genetic diseases are frequently used as gene markers, with the disease state being one allele and the healthy state the second allele.
		In this case, the value of the genetic map is that an inherited disease can be located on the map by following the inheritance of a DNA marker present in affected individuals but absent in unaffected individuals, although the molecular basis of the disease may not yet be understood, nor the gene(s) responsible identified.
		Genetic maps are also used to generate the essential backbone, or scaffold, needed for the creation of more detailed human genome maps.
	www.ncbi.nlm.nih.gov /About/primer/mapping.html (2961 words)

	TH&T \| Publications \| Article Search Results
		In addition, H.R. 3967 would require that a patent applicant publicly disclose genetic sequence information within thirty days of filing a patent application claiming the sequence if federal funds were used in the development of the sequence.
		In their view, the proposed legislation would alleviate the negative impact by providing an exemption for researchers who are not “directly engaged in the commercial manufacture, commercial sale, or commercial offer for sale of a drug, medical device, or other product” that is based upon the patented genetic sequence information.
		H.R. 3967 is intended to address these concerns by providing a limited exemption for certain “genetic diagnostic, prognostic, or predictive” testing that would otherwise infringe a patent covering genetic sequence information.
	www.tht.com /pubs/SearchMatchPub.asp?ArticleID=829 (551 words)

	New Scientist Breaking News - Genetic sequence of SARS virus revealed
		The genetic sequence is vital to developing tests for the infection, and drugs and vaccines to treat it.
		The lab usually studies genetic changes in cancer, but it switched to work 24 hours a day on SARS after virus taken from a case in Toronto was cultured.
		The sequence confirms earlier screening results that a loop at the 3' end of the RNA appears identical to one in the Avian Infectious Bronchitis virus, which infects turkeys and chickens.
	www.newscientist.com /article.ns?id=dn3623 (527 words)

	UNRAVELING THE DNA MYTH The spurious foundation of genetic engineering Barry Commoner / Harper's Magazine Feb02
		The wonders of genetic science are all founded on the discovery of the DNA double helix-by Francis Crick and James Watson in 1953-and they proceed from the premise that this molecular structure is the exclusive agent of inheritance in all living things: in the kingdom of molecular genetics, the DNA gene is absolute monarch.
		According to Crick's sequence hypothesis, the gene's nucleotide sequence (i.e., its "genetic information") is transmitted, altered in form but not in content, through RNA intermediaries, to the distinctive amino acid sequence of a particular protein.
		In alternative splicing, however, the gene's original nucleotide sequence is split into fragments that are then recombined in different ways to encode a multiplicity of proteins, each of them different in their amino acid sequence from each other and from the sequence that the original gene, if left intact, would encode.
	www.mindfully.org /GE/GE4/DNA-Myth-CommonerFeb02.htm (6389 words)

	Genetic Mutations (Site not responding. Last check: 2007-10-09)
		The new sequence may not be viable to produce an organism, depending on which genes are reversed.
		Similar to the effects of deletion, where a nucleotide is inserted into a genetic sequence and therefore alters the chain thereafter.
		All of the genetic mutations looked at through the last 2 pages more or less have a negative impact and are undesired, however, in some cases they can prove advantageous.
	www.biology-online.org /2/8_mutations.htm (389 words)

	USATODAY.com - Groups publish SARS' genetic sequence (Site not responding. Last check: 2007-10-09)
		WASHINGTON (AP) — Genetic sequences of the SARS virus were hurried into print Thursday in an effort to help researchers worldwide in their efforts to find drugs to treat the respiratory disease or a vaccine to prevent it.
		The sequences were posted on the Internet on April 15 but are only now being peer-reviewed, a scientific step that lends credence to the accuracy of the work.
		The sequences were mapped on a crash basis by the two teams of researchers in an effort to distribute the data to other scientists and to drug companies as soon as possible, said Pallansch.
	www.usatoday.com /news/health/2003-05-01-sars-genetic-sequence_x.htm (646 words)

	Methods in genetic sequencing, DNA analysis and gene cloning !!
		When DNA has be removed, the genetic material has to be purified, for genetic material of high molecular weight, Phenol can be added to the insoluble solution that has been obtained.
		Although the sequence of bases in genetic material are not randomly distributed as genes are related and sequences conserved this specific site recognition lowers the number of cutting sites on a genome considerably.
		Increasingly there are many uses for such genetic manipulation, by inserting the gene that codes for human insulin in to bacteria, they will begin to create the insulin protein and provide a useful drug for those with diabetes.
	www.geocities.com /SiliconValley/5504/biochem.html (2130 words)

	genome.gov \| 2003 Release Mechanism Preserves Y Chromosome Gene
		All other chromosomes occur in pairs and preserve genetic integrity by exchanging information with matching genes on the homologous chromosome, a process called "crossing over." But the Y chromosome lacks that option, being the only chromosome that is unpaired.
		This phenomenon, called gene conversion - the non-reciprocal transfer of genetic information from one DNA molecule to another -- has been previously observed on a small scale over long evolutionary timescales between repeated sequences on the same chromosome, but not at the dramatic frequency apparently employed by the Y chromosome.
		The entire project, including genetic mapping, technology development, the study of model organisms, and the ethical, legal and social implications (ELSI) program was initially projected to take 15 years, but was completed more than two years early at a cost that was $400 million less than expected.
	www.genome.gov /11007628 (694 words)

	First Complete Plant Genetic Sequence Is Determined ANDREW POLLACK / New York Times 14dec00
		The plant, Arabidopsis thaliana, is a diminutive weed that is related to the mustard plant and is worthless as a crop.
		Scientists are expected to publish the full sequence of the human genome early next year; genomes completed previously include the fruit fly, the C. eleganis worm and yeast.
		The genome consists of 5 pairs of chromosomes containing about 125 million base pairs, the units of the genetic code that are represented by the letters A,C,G and T. That is considerably smaller than the human genome, which has 23 pairs of chromosomes and 3.1 billion base pairs.
	www.mindfully.org /GE/First-Complete-Plant.htm (1153 words)

	Genetic sequence identified for anti-bacterial sea slug protein (Site not responding. Last check: 2007-10-09)
		Genetic sequence identified for anti-bacterial sea slug protein
		ATLANTA (April 29, 2004) -- A Center for Behavioral Neuroscience research team led by Georgia State University biologist Charles Derby has identified the genetic sequence of an anti-microbial protein called Escapin found in the ink of the common Aplysia sea slug or hare.
		Derby, who has filed a provisional patent for Escapin's genetic sequence, plans to submit an academic paper for publication on the protein within the next several months.
	www.eurekalert.org /pub_releases/2004-04/euhs-gsi042904.php (328 words)

	GENETIC DISEASES; GLOSSARY (Site not responding. Last check: 2007-10-09)
		Complementary sequences: Nucleic acid base sequences that can form a double-stranded structure by matching base pairs; the complementary sequence to G-T-A-C is C-A-T-G. Conserved sequence: A base sequence in a DNA molecule (or an amino acid sequence in a protein) that has remained essentially unchanged throughout evolution.
		Exons: The protein-coding DNA sequences of a gene.
		Sequence tagged site (STS): Short (200 to 500 base pairs) DNA sequence that has a single occurrence in the human genome and whose location and base sequence are known.
	www.bioscience.org /atlases/disease/genedis/glossary.htm (3886 words)

	DNA sequence - Wikipedia, the free encyclopedia
		A succession of any number of nucleotides greater than four is liable to be called a sequence.
		With regard to its biological function, which may depend on context, a sequence may be sense or anti-sense (see DNA), and either coding or noncoding.
		This page was last modified 05:58, 3 September 2005.
	en.wikipedia.org /wiki/DNA_sequence (78 words)

	Neurospora crassa Genetic Map Description
		Most of the available marker sequence is from Neurospora crassa itself, but in some cases the sequence is derived from a homologous gene in Saccharomyces cerevisiae.
		All genetic markers with associated sequence were compared to the current assembly using BLASTN.
		This may mean that the marker is not in the current assembly, or that the BLASTN results did not point to a unique location in the genome.
	www.broad.mit.edu /annotation/fungi/neurospora_crassa_6/markers.html (740 words)

	Genetics moves on
		The Human Genome Project is decoding, letter by letter, the sequence of 3 billion nucleotide bases in the human genome.
		This gibberish, a bit of genetic sequence, is nonetheless the biggest story in biology.
		Three prominent genetic scientists laid out their vision for the future of genomics in November, 1998, in talks at the New Horizons in Science meeting, hosted by Boston University.
	whyfiles.org /075genome (308 words)

	Philosophy and Definition for a Universal Genetic Sequence Database 1
		Both sequences are reported but the recessive variant is not documented as a mutation, although this was known from another source.
		Sequence objects that are not entered into the database should not be considered discoveries, just as an invention is not a patent until it is published by the Patent Office.
		The region separating sequence piece 1 (line segment p1) and piece 2 (p2) is dashed to indicate that it is not sequenced.
	www-lmmb.ncifcrf.gov /~toms/paper/philgen/latex/paper.html (9886 words)

	Genetic Code (Site not responding. Last check: 2007-10-09)
		The genetic code refers to how the gene sequence in translated into protein sequence.
		There are 20 different amino acids in human proteins so some amino acids are encoded for by more than one codon (this is refered to redundancy of the genetic code).
		The figure on the right shows how a genetic sequence could be translated three different ways depending on where you decided to start.
	www.uvm.edu /~cgep/Education/GeneticCode.html (276 words)

	A Glossary for Molecular Information Theory and the Delila System
		Both of the properties of averaging and additivity are important for sequence logos and sequence walkers.
		Rogan and Schneider (1995) a case is shown where a patient was misdiagnosed because a consensus sequence was used to interpret a sequence change in a splice junction.
		Note that sequence logos are an average picture of a set of binding sites (which is why logos can have several letters in each stack) while sequence walkers are the individuals that make up that average (which is why walkers have only one letter per position).
	www.lecb.ncifcrf.gov /~toms/glossary.html (10565 words)

	Efficiency of Shared-Memory Multiprocessors for a Genetic Sequence Similarity Search Algorithm
		As biologists gather more sequence data, sequence similarity algorithms are more and more useful, but take longer and longer to run.
		BLAST is one of the most popular sequence similarity algorithms in use today, but its running time is proportional to the size of the database.
		Sequence similarity analysis using BLAST is becoming a bottleneck.
	www-users.cs.umn.edu /~echi/papers/perf/perf.html (277 words)

	Mutations
		The genetic sequence is shown in fl while the protein sequence is in blue.
		This can occur because of redundancy in the genetic code where an amino acid may be encoded for by multiple codons.
		A change in the genetic sequence that occurs at the boundary of the exons and introns.
	www.uvm.edu /~cgep/Education/Mutations.html (473 words)

	Efficiency of Shared-Memory Multiprocessors for a Genetic Sequence Similarity Search Algorithm - Chi, Shoop, Carlis, ... (Site not responding. Last check: 2007-10-09)
		GenBank, the primary repository for DNA sequence data is doubling in size every 1.3 years.
		One of the most successful techniques for analyzing genetic data is sequence similarity analysis---the comparison of unknown sequences against known sequences kept in databases.
		Short sequences that used to take 5 10 minutes can be done in tens of seconds.
	citeseer.ist.psu.edu /chi97efficiency.html (561 words)

	Verbumculus Sequence Analyzer (Site not responding. Last check: 2007-10-09)
		In most approaches to the detection of unusual frequencies of words in sequences, the words (up to a certain length) are enumerated more or less exhaustively and individually checked in terms of observed and expected frequencies, variances, and scores of discrepancy and significance thereof.
		We take instead the global approach of annotating a suffix trie or automaton of a sequence with some such values and scores, with the objective of using it as a collective detector of all unexpected behaviors, or perhaps just as a preliminary filter for words suspicious enough to warrant further and more accurate scrutiny.
		Analysis of the upstream sequences of the Early(I) cluster from the
	www.cs.ucr.edu /~stelo/Verbumculus (560 words)

	HIV Databases
		The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials.
		A new search interface is now available that allows the user to directly align and analyze database search results, selected subtype reference sequences and aligned user sequences.
		In case of building a tree, the user can also choose to add the subtype reference sequences and combine all three sets (user provided alignment, search results and subtype reference sequences) to build a tree.
	hiv-web.lanl.gov (301 words)

	About GeneCards (Site not responding. Last check: 2007-10-09)
		GeneTests (formerly GeneClinics): a clinical information resource relating genetic testing to the diagnosis, management, and genetic counseling of individuals and families with specific inherited disorders.
		The Genetic Association Database (GAD) is an archive of human genetic association studies of complex diseases and disorders.
		is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
	www.genecards.org /background.shtml (2218 words)

	Scientists Crack SARS Genetic Sequence (Site not responding. Last check: 2007-10-09)
		Summary Scientists have cracked the genetic sequence of the virus believed to cause severe acute respiratory syndrome (SARS).
		Scientists have cracked the genetic sequence of the virus believed to cause severe acute respiratory syndrome (SARS).
		A third explanation suggests that an animal virus underwent "recombination" (an exchange of genetic material) with other coronaviruses, allowing it to infect humans and cause disease.
	news.nationalgeographic.com /news/2003/04/0415_030415_sarsdna.html (671 words)

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