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Topic: Nucleotide sequences

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	Examination of Patent Applications Containing Nucleotide Sequences
		Nucleotide sequences encoding different proteins are structurally distinct chemical compounds and are unrelated to one another.
		These sequences are thus deemed to normally constitute independent and distinct inventions within the meaning of 35 U.S.C. Absent evidence to the contrary, each such nucleotide sequence is presumed to represent an independent and distinct invention, subject to a restriction requirement pursuant to 35 U.S.C. § 121 and 37 CFR 1.141 et seq.
		Nucleotide sequences encoding the same protein are considered to satisfy the unity of invention standard and will continue to be examined together.
	www.uspto.gov /web/offices/com/sol/og/1996/seqexam.htm (1437 words)

	United States Patent Application: 0040197895
		The method of claim 12, wherein said second nucleotide sequence further comprises at least one modification of the nucleotide sequence encoding AAV VP1 capsid protein selected from among a G at nucleotide position 12, an A at nucleotide position 21, and a C at nucleotide position 24.
		A determination of the degree of homology of two nucleic acids sequences is a determination of the percentage of time a nucleotide, from among the four known natural nucleotides, exactly matches a counterpart on a second nucleotide sequence, e.g.
		This consisted of the substitution of the nucleotide sequence immediately upstream of VP1 with a particular nine nucleotide sequence and the change of the initiator (first) codon of VP1 from methionine to threonine by an T to C mutation at position 2 of the coding nucleotide sequence.
	appft1.uspto.gov /netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PG01&p=1&u=/netahtml/PTO/srchnum.html&r=1&f=G&l=50&s1="20040197895".PGNR.&OS=DN/20040197895&RS=DN/20040197895 (15398 words)

	World Intellectual Property Organization (Site not responding. Last check: 2007-10-09)
		For example, using this approach, sequence motifs encoding a domain of interest may be shuffled between the sunflower PR5-2 or BAP nucleotide sequences of the invention and other known anti-pathogenic sequences to obtain new sequences encoding a polypeptide with an improved property of interest, such as a broader spectrum of pathogen resistance.
		It is recognized that having identified the nucleotide sequences for the promoter regions disclosed herein, it is within the state of the art to isolate and identify further regulatory elements in the 5'untranslated region upstream from the particular promoter regions identified herein.
		Sequences isolated based on their sequence identity to the entire BAB or PR5-2 promoter sequences and the BAP or PR5-2 nucleotide sequences of the present invention or to fragments thereof are encompassed by the present invention.
	www.wipo.int /ipdl/IPDL-CIMAGES/view/pct/getbykey5?KEY=01/27298.010419&ELEMENT_SET=DECL (8764 words)

	Hypertext MPEP: 803.04 Restriction - Nucleotide Sequences
		These sequences are thus deemed to normally constitute independent and distinct inventions within the meaning of 35 U.S.C. Absent evidence to the contrary, each such nucleotide sequence is presumed to represent an independent and distinct invention, subject to a restriction requirement pursuant to 35 U.S.C. and 37 CFR 1.141 et seq.
		See MPEP § 1850 for treatment of claims containing independent and distinct nucleotide sequences in international applications filed under the Patent Cooperation Treaty (PCT) and national stage applications filed under 35 U.S.C. Examples of typical nucleotide sequence claims impacted by the partial waiver of 37 CFR 1.141 et seq.
		Only the ten nucleotide sequences selected in response to the restriction requirement and any other claimed sequences which are patentably indistinct therefrom will be examined.
	patents.ame.nd.edu /mpep/8/803.04.html (801 words)

	United States Patent: 6,506,594
		Sequences are read by hybridization of segments of the target DNA to the oligonucleotides and assembly of overlapping segments of hybridized oligonucleotides.
		Here, the presence of the A and C alleles in the target nucleotide sequences is indicated due to the fluorescence at the addresses on the solid support with capture oligonucleotide probes complementary to portions Z1 and Z3, respectively.
		The amount of target nucleotide sequences in the sample is then determined by comparing the amount of captured ligated product generated from known amounts of marker target nucleotide sequences with the amount of other ligated product sequences captured.
	grendel.med.cornell.edu /pat6506594.htm (13236 words)

	[No title]
		These sequences are thus deemed to normally constitute independent and distinct inventions within the meaning of 35 U.S.C. Absent evidence to the contrary, each such nucleotide sequence is presumed to represent an independent and distinct invention, subject to a restriction requirement pursuant to 35 U.S.C. and 37 CFR 1.141.
		In establishing the new policy, the Commissioner has partially waived the requirements of 37 CFR 1.141 and will permit a reasonable number of such nucleotide sequences to be claimed in a single application.
		Nucleotide sequences encoding the same protein are not considered to be independent and distinct and will continue to be examined together.
	www.uspto.gov /web/offices/pac/mpep/documents/2400_2434.htm (369 words)

	Co-existence of recent and ancestral nucleotide sequences in viral quasispecies of human immunodeficiency virus type 1 ...
		Nucleotide distance (D) to a Spanish consensus was calculated by the Kimura two-parameter model in 96 Spanish HIV-1 subtype B V3 nucleotide sequences and plotted against the sequence sampling year.
		Nucleotide sequence clusters within each patient are grouped by vertical lines and denominated by lower-case letters a, b and c.
		Sequences are shown with the following symbols with reference to the baseline clone 7.98: dots (.), identity with 7.98 clone; hyphens (-), gap inserted to maintain alignment of sequence; replacements are indicated by the appropriate code letter.
	vir.sgmjournals.org /cgi/content/full/85/2/399 (4498 words)

	Incomplete nucleic acid sequences
		Authors should always, however, make it clear which strand of DNA or RNA a given sequence refers to, and in circumstances where confusion between DNA and RNA is likely the sequence may be prefixed with the lower-case letter d or r, as in the previous recommendations [1].
		For instance, sequences recognised by the RNA polymerase of Escherichia coli may be presented as the juxtaposition of two sequences 5'-AA(A or T)NTNNN(C or G)TTGACA-3' and 5'-(T or G)NNTATAAT-3' separated by 13 to 16 nucleotides (adapted from [15, 16]), where N represents any nucleotide.
		Examples are given whereby the nomenclature is applied to sequences recognised by certain type II restriction endonucleases (Table 3) and to uncertainties in deriving a nucleic acid sequence from the corresponding amino acid sequence (Table 4).
	www.chem.qmul.ac.uk /iubmb/misc/naseq.html (2915 words)

	FrameSearch
		For each sequence comparison, the program creates the optimal local alignment of the best region of similarity between the protein sequence and all possible codons on each strand of the nucleotide sequence.
		MotifSearch uses a set of profiles (representing similarities within a family of sequences) as a query to either a) search a database for new sequences similar to the original family, or b) annotate the members of the the original family with details of the matches between the profiles and each of the members.
		Normally, if one of the sequences is aligned opposite gap characters for one or more complete lines of the alignment, then that portion of the alignment is abbreviated with three dots arranged in a vertical line.
	mcrcr0.med.nyu.edu /gcg/framesearch.html (5419 words)

	Estimating Evolutionary Distances from Nucleotide Sequences
		In addition, we will see how these distances can be written in a file in various formats through options for page size, precision, and relative placement of distances and their standard errors.
		We have computed nucleotide distances from the nucleotide sequence data in the file Drosophila_Adh.meg.
		As with the previous nucleotide estimation a results viewer window will be displayed, showing the distances in a grid format.
	www.megasoftware.net /WebHelp/walk_through_mega/estimating_evolutionary_distances_from_nucleotide_sequences.htm (298 words)

	PatScan -- Locating Patterns in Nucleotide Sequences
		PatScan currently uses a subset of Release 60 of the EMBL Nucleotide Sequence Database maintained by EBI.
		Match 12 characters of a 3-character sequence occuring 4 times with up to 1 mismatch in each of the the 2nd, 3rd and 4th sequences.
		Note that complex patterns could often match against a number of overlapping areas of a sequence: only the first would be reported (after a successful match, the matching algorithm picks up at the first character past the matched substring).
	www.mcs.anl.gov /compbio/PatScan/HTML/matching_nucleotides.html (825 words)

	DNADIST -- Program to compute distance matrix from nucleotide sequences
		For the DNAML model, or for any of the models where one or both sequences contain at least one of the other ambiguity codons such as Y, R, etc., a maximum likelihood calculation is also done using code which was originally written for DNAML.
		Each sequence starts on a new line, has a ten-character species name that must be blank-filled to be of that length, followed immediately by the species data in the one-letter code.
		The sequences must either be in the "interleaved" or "sequential" formats described in the Molecular Sequence Programs documentation.
	cmgm.stanford.edu /phylip/dnadist.html (3090 words)

	MetaDB: Nucleotide Sequences: Transcriptional Regulator Sites and Transcription Factors Databases List
		AtcisDB consists of the 5' regulatory sequences of all 29,388 annotated genes with a description of the corresponding cis-regulatory elements.
		The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions.
		The option allowing nucleotide sequences to be searched for according to their homology using BLAST is also included.
	www.neurotransmitter.net /metadb/index.php?catid=20 (5840 words)

	The EMBL Nucleotide Sequence Database
		Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications.
		Each of the three groups collects a portion of the total sequence data reported worldwide, and all new and updated database entries are exchanged between the groups on a daily basis.
		The Nucleotide Sequence Database is also produced in collaboration with the DNA Database of Japan (DDBJ).
	www.ebi.ac.uk /embl (317 words)

	MetaDB: Nucleotide Sequences: International Nucleotide Sequence Database Collaboration Databases List
		The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources.
		New and updated data records are distributed daily and the whole EMBL Nucleotide Sequence Database is released four times a year.
		Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data.
	www.neurotransmitter.net /metadb/index.php?catid=17 (564 words)

	HIV-1 and HIV-2 LTR Nucleotide Sequences: Assessment of the Alignment by N-block Presentation, "Retroviral Signatures" ...
		HIV-1 and HIV-2 LTR Nucleotide Sequences: Assessment of the Alignment by N-block Presentation, "Retroviral Signatures" of Overrepeated Oligonucleotides, and a Probable Important Role of Scrambled Stepwise Duplications/Deletions in Molecular Evolution -- Laprevotte et al.
		HIV-1 and HIV-2 LTR Nucleotide Sequences: Assessment of the Alignment by N-block Presentation, "Retroviral Signatures" of Overrepeated Oligonucleotides, and a Probable Important Role of Scrambled Stepwise Duplications/Deletions in Molecular Evolution
		The hatched zones correspond to the flanking eukaryotic sequences and the Nef gene-coding sequence.
	mbe.oxfordjournals.org /cgi/content/full/18/7/1231 (7198 words)

	translate nucleotide sequences (Site not responding. Last check: 2007-10-09)
		Those nucleotides that are translated into amino acids are shown in fl (exons) and untranslated nucleotides are shown in gray (introns, UTRs).
		Above the text field rulers for the nucleotide positions and the translated amino acids are shown.
		Atutomated translation of nucleotides into amino-acid sequences is possible with the dialog Translating DNA using GeneBank files.
	www.charite.de /bioinf/strap/doc/EditDnaParentPane.html (287 words)

	EBI Databases
		EMBL Nucleotide Database - Europe’s primary collection of nucleotide sequences is maintained in collaboration with Genbank (USA) and DDBJ (Japan)
		The EMBL Nucleotide Sequence Database was frozen to make Release 84 on 24-AUG-2005 The release contains 58,758,902 sequence entries comprising 107,562,580,723 nucleotides,of which 11,106,066 entries (55,608,219,735 nucleotides) are WGS (whole genome shotgun) data.....
		PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains.
	www.ebi.ac.uk /Databases (898 words)

	Estimation of evolutionary distance from nucleotide sequences (Site not responding. Last check: 2007-10-09)
		Estimation of evolutionary distance from a pair of nucleotide sequences is a key component of some commonly-used phylogenetic reconstruction procedures.
		Evolutionary distance is typically defined in the context of a stochastic model for nucleotide substitution, the simplest such model being the single-rate model of Jukes and Cantor (1969).
		The bias reduction method corresponds to penalizing the likelihood by a suitable imprecise prior, and is found to be much more stable than the near-unbiased estimator suggested previously by Tajima (1993).
	www.stats.bris.ac.uk /Seminars/seminars_files/Abstracts/firth.html (225 words)

	Long-range correlations in nucleotide sequences [see comments] (Site not responding. Last check: 2007-10-09)
		DNA sequences have been analysed using models, such as an n-step Markov chain, that incorporate the possibility of short-range nucleotide correlations.
		We propose here a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which we term a 'DNA walk'.
		Thus we uncover in the nucleotide sequence a remarkably long- range power law correlation that implies a new scale-invariant property of DNA.
	reylab.bidmc.harvard.edu /publications/Nat/pbghsss-92.html (164 words)

	Computing Statistical Quantities for Nucleotide Sequences
		In addition, we explain shortcuts for obtaining frequently used commands, methods of accessing on-line help, and the distinction between enabled and disabled commands.
		DNA sequences are displayed on the screen in a grid format.
		Once the sequences are translated, calculate the amino acid composition by selecting the
	www.megasoftware.net /WebHelp/walk_through_mega/computing_statistical_quantities_for_nucleotide_sequences.htm (520 words)

	Reverse Complement Many Nucleotide Sequences
		Please enter a sequence or sequences in the box above consisting of the letters A,C,G,T,U or N or the degenerate code as listed below.
		Sequence should be in FASTA format (click example).
		MolBiol.Net Warning - Your browser may crash when you input sequences of more than several thousand base pairs in length.
	www.bioinformatics.vg /bioinformatics_tools/batch_reverse_complement.shtml (208 words)

	[Bioperl-l] Applying pairwise Smith-Waterman on nucleotide sequences? (Site not responding. Last check: 2007-10-09)
		Previous message: [Bioperl-l] Applying pairwise Smith-Waterman on nucleotide sequences?
		See: http://bioperl.org/pipermail/bioperl-l/2002-February/007281.html There is a description of how to run EMBOSS's 'water' from within Bioperl in the FAQ http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/FAQ?rev=1.14andcvsroot=bioperlandcontent-type=text/vnd.viewcvs-markup -j On Thu, 6 Jun 2002, Danny Yoo wrote: > Hi everyone, > > Hope this isn't a silly questions: I've been trying to get Bio::Tools::pSW > working on some nucleotide sequences I have.
		> > Warning Error > Sequence seq2 is not typed as protein...
	www.bioperl.org /pipermail/bioperl-l/2002-June/008086.html (191 words)

	Nucleotide Sequences 1986/1987: Other Vertebrates and Invertebrates:0125125135:Atencio, Edwin J.:eCampus.com
		Nucleotide Sequences 1986/1987: Other Vertebrates and Invertebrates:0125125135:Atencio, Edwin J.:eCampus.com
		Nucleotide Sequences 1986/1987: Structural Rna, Synthetic, and Unannotated Sequences
		Nucleotide Sequences 1986/1987: Database Directory and Master Indices
	www.ecampus.com /bk_detail.asp?isbn=0125125135 (35 words)

	[No title]
		1793 nucleotide sequences listed for all 3 species
		355 nucleotide sequences listed for all 3 species
		344 nucleotide sequences listed for all 3 species
	www.ictvdb.rothamsted.ac.uk /AusGroupFamilies.htm (328 words)

	Translate the nucleotide sequences from 3. (Site not responding. Last check: 2007-10-09)
		subtypeB specific sequence R A F Y A
		to the three dimensional structure by sending your protein sequences to the appropriate site.
		The three dimensional structure of each V3 loop should be displayed by the PDB viewer.
	pioneer.netserv.chula.ac.th /~satchasa/H9.htm (142 words)

	Gibbs Sampling for nucleotide sequences (Site not responding. Last check: 2007-10-09)
		Input sequence sample to be aligned (sequnces must be in fasta format and no longer then 100 kB):
		L., Neuwald A. F., Wootton J. C., Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
		This resource has been developed in the Institute of Cytology and Genetics, Novosibirsk, Russia
	wwwmgs.bionet.nsc.ru /mgs/programs/gibbs_nuc (59 words)

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