
	Where results make sense

Topic: Sequence database

Related Topics

Sequence analysis

Sequence alignment

Blast

Sequence motif

Repeated Sequences

Sequencing

Hidden Markov model

Genetic code

Gene regulatory network

Markov process

Lac operon

Bayesian network

Operon

In the News (Wed 11 Nov 09)

Northern Trust

Marvin Harrison

Peter Chernin

Gary Locke

Match Play

Penelope Cruz

Mickey Rourke

AR Rahman

Danny Boyle

Hugh Jackman

	Comprehensive Curated Prion Sequence Database
		Point mutations, octapeptide deletions and insertions, and upstream and downstream non-coding regions are dealt with at greater length elsewhere, as are major topics such as the significance of sheep and cow alleles in disease.
		In some cases, eg N171S, the database suggests that a mutation in human that is normal in other lineages (here chimpanzee) is probably not pathogenic; history of a codon position supplements 3D structure and extensive data elsewhere in evaluating conservativeness of amino acid substitutions.
		Sequence data resides within a single flat-file database (matrix) of 231 fields (columns) x 479 sequence records (rows) containing 278,000 characters when saved as a text file.
	www.mad-cow.org /00/seq_resource_00.html (3770 words)

	Sequence database - Wikipedia, the free encyclopedia
		A database can include sequences from only one organism, as in databases including all the proteins in 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.
	en.wikipedia.org /wiki/Sequence_database (314 words)

	NCBI Third Party Annotation Sequence Database
		For example, sequences with Accession Numbers such as NT_112233 or NW_123456 represent contig sequences; the sequences used to assemble these contigs, which can be found at the bottom of contig records, should be cited in a TPA sequence submission.
		Sequences with Accession Numbers such as XM_345678 or NM_123456 are RefSeqs representing mRNAs that are not experimentally determined and therefore cannot be cited as primary data.
		TPA sequences are held confidential until their Accession Numbers or sequence data and/or annotation appear in a peer-reviewed publication in a biological journal.
	www.ncbi.nlm.nih.gov /Genbank/TPA.html (915 words)

	Compilation of tRNA sequences and sequences of tRNA genes
		Positions in particular sequence which are not filled (gaps in the generalised structure) are indicated by a dash.
		Each sequence in the Compilation of tRNA Sequences and Compilation of tRNA Genes has unique six-position identification code of the sequence ('D' or 'R' for DNA or RNA, respectively; a one-letter code for the amino acid, X for methionine-initiator, Z for selenocysteine; the three-digit code specifying the organism and one digit for isoacceptor number).
		It is possible to scroll the found sequences one by one or to select directly the sequence of interest from the result table.
	www.uni-bayreuth.de /departments/biochemie/trna (1010 words)

	Swiss-Prot Annotated protein sequence database
		Sequence entries are composed of different line-types, each with their own format.
		In Swiss-Prot, as in most other sequence databases, two classes of data can be distinguished: the core data and the annotation.
		It is important to provide the users of biomolecular databases with a degree of integration between the three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as with specialized data collections.
	www.expasy.org /sprot/sprot_details.html (478 words)

	Citations: A RAPID algorithm for sequence database comparisons: application to the identification of vector ... (Site not responding. Last check: 2007-10-03)
		....that the space requirement of a database resident SBST is approximately 50 of that of the suffix tree.
		Database indexing for large DNA and protein sequence..
		Miller, C., J. Gurd, and A. Brass, A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases.
	citeseer.ist.psu.edu /context/1641723/0 (554 words)

	The PIR-International Protein Sequence Database - George, Barker, Mewes, Pfeiffer, Tsugita (ResearchIndex) (Site not responding. Last check: 2007-10-03)
		Since 1988 the database has been maintained collaboratively by PIR-International, an international association of data collection centers cooperating to develop this resource during a period of explosive growth in new...
		Sequences in PIR are first classified by homeomorphic domains, that is, into...
		The PIR-International Protein Sequence Database - Barker, Garavelli, Haft..
	citeseer.ist.psu.edu /506881.html (549 words)

	HCV database home page (Site not responding. Last check: 2007-10-03)
		About this database The Hepatitis C Virus (HCV) database project is funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID).
		This project is deeply indebted to the HIV database group, led by Dr. Bette Korber, for much of its tools, infrastructure and philosophy; the two databases continue to collaborate closely and to share software and resources.
		Since the publication of the the new HCV nomenclature proposal, the HCV database has switched to using the H77 sequence as a reference sequence, instead of HCV-H. The main advantage of H77 is that its 3' UTR is much longer.
	hcv.lanl.gov /content/hcv-db/index (411 words)

	The EMBL Nucleotide Sequence Database
		The database is produced in an international collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ).
		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 current database release (Release 90, March 2007), with according Release notes and user manual are available from the EBI servers.
	www.ebi.ac.uk /embl (310 words)

	HPV Database (Site not responding. Last check: 2007-10-03)
		The new relational Papillomavirus database is an extension of the HPV compendiums published in 1994, 1995, 1996 and 1997, which will remain available in electronic form.
		At the core of the database is the table of annotated records, one for each unique papillomavirus type.
		In addition to the search capacity, analysis tools are included for use with sequences in the database or sequences provided by the user.
	hpv-web.lanl.gov /stdgen/virus/hpv (242 words)

	[No title]
		Their presence at this extreme end of the distribution indicates that there is much greater and significant similarity between these sequences and the query sequence than between general sequences in the database and the query sequence.
		Sequences that have an initn score larger than a cutoff value (usually 50 but this can be altered with a "LIST n" command in the query file) are then used for a Smith-Waterman alignment (see the section on alignments) and an OPT score is generated from these alignments.
		PROSITE database to search the query sequence (must be protein or optionally, it will translate your nucleotide sequence to a protein) for similar protein motifs.
	helix.biology.mcmaster.ca /721/access.html (9601 words)

	HCV Sequence Database
		The Hepatitis C Virus (HCV) sequence database is a project funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID).
		We strive to present HCV sequences and associated data in a userfriendly way, by providing access to the central database via a web-accessible search interface and supplying a number of analysis tools.
		The HCV database is deeply indebted to the HIV database, led by Dr. Bette Korber, for much of its tools, infrastructure and philosophy; the two databases continue to collaborate closely and to share software and resources.
	www3.oup.co.uk /nar/database/summary/492 (172 words)

	Sequence Database Group Home Page
		The Sequence Database group is an amalgamation of activities related to the production of protein sequence, protein family and nucleotide sequence databases at the EBI.
		The Sequence Database group is headed by Rolf Apweiler.
		The Alternative Splicing Database (ASD) Project aims to understand the mechanism of alternative splicing on a genome-wide scale by creating a database of alternatively spliced exons from human, and other model species.
	www.ebi.ac.uk /seqdb/index.html (217 words)

	Antiinfective Peptides Laboratory - Prof. Alessandro Tossi
		protein sequences database to wich they are hyperlinked.
		The database is extended with sequences obtained from the literature, from literature searches, or from translates of nucleic acid sequences as present in the EMBL database.
		The database was originally created as part of the thesis work of undergraduate students, under the supervision of Dr. Alex Tossi.
	www.bbcm.univ.trieste.it /~tossi/pag1.htm (268 words)

	nrdb90: a nonredundant sequence database (Site not responding. Last check: 2007-10-03)
		nrdb90 clusters the sequence database yielding a representative subset that is faster to search and improves the consistency of sequence annotation.
		Search space is pruned using deca- and pentapeptide composition filters that leave a minimal fraction of pairs for which sequence identity is determined by explicit alignment.
		The union of the Swissprot, Swissnew, Trembl, Tremblnew, Genbank, PIR, Wormpep and PDB databases, containing 260,000 non-duplicate sequences, was processed in 2 days CPU time and yielded a representative set at 90 % sequence identity with a size reduction of 46 %.
	www.embl-ebi.ac.uk /~holm/nrdb90 (194 words)

	Sequence database -- Facts, Info, and Encyclopedia article (Site not responding. Last check: 2007-10-03)
		Sequence database -- Facts, Info, and Encyclopedia article
		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.
		The (A long and hard-hit fly ball) BLAST program is a method of this type.
	www.absoluteastronomy.com /encyclopedia/s/se/sequence_database.htm (300 words)

	EMBL Nucleotide Sequence Database
		The EMBL Nucleotide Sequence Database (URL: http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA).
		Data is exchanged amongst the collaborating databases on a daily basis.
		The major contributors to the EMBL database are individual authors and genome project groups.
	www3.oup.co.uk /nar/database/summary/2 (137 words)

	Sequiviridae Sequence Database (Site not responding. Last check: 2007-10-03)
		Isogai, M., Cabauatan, P.Q., Masuta, C., Uyeda, I., Azzam, O. Complete nucleotide sequence of the rice tungro spherical virus genome of the highly virulent strain Vt6.
		Turnbull-Ross, A.D., Reavy, B., Mayo, M.A., Murant, A.F. The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus.
		Zhang, S., Davies, J.W. and Hull R. Sequences of the three coat protein genes of a Malaysian isolate of rice tungro spherical virus reveal a close relationship to the Philippine isolate.
	www.iah.bbsrc.ac.uk /virus/Sequiviridae (241 words)

	MRC HGU - MuStaR(TM) Sequence Variant Database Software
		Curation Program: A relational database written in MS-Access, used only by the Curator to add/modify records, to import new submissions made via the web form, and to export the database in a form for the web search engine and control panel to use.
		The database is protected by password, but otherwise depends on the security employed on the PC running the software.
		The purpose of distributing a database on the web is to make it accessible to a wide range of people.
	www.hgu.mrc.ac.uk /Softdata/Mustar (1765 words)

	CORBA and the EMBL Nucleotide Sequence database (Site not responding. Last check: 2007-10-03)
		As a result of this, the Nucleotide Sequence database is divided up in to (currently) 4 parts, each of which is served by a different servers.
		They should be thought of as separate databases.
		This division is not final, e.g., it is conceivable that "sequence features" becomes a separate database.
	corba.ebi.ac.uk /EMBL_embl.html (165 words)

	Sequence database searching (Site not responding. Last check: 2007-10-03)
		The most obvious first stage in the analysis of any new sequence is to perform comparisons with sequence databases to find homologues.
		A very important thing to do, and one which is sometimes overlooked, is to compare any new sequence to a database of sequences for which 3D structure information is available.
		Whether or not your sequence is homologous to a protein of known 3D structure is not obvious in the output from many searches of large sequence databases.
	www.bmm.icnet.uk /people/rob/CCP11BBS/dbsearch.html (636 words)

	miRBase::Sequences
		The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation.
		Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).
		Please note that the predicted stem-loop sequences in the database are not strictly precursor miRNAs (pre-miRNAs), but include the pre-miRNA and some flanking sequence from the presumed primary transcript.
	microrna.sanger.ac.uk /sequences (368 words)

	ISD: Influenza Sequence Database at LANL
		The Influenza Sequence Database (ISD) contains all published influenza viral sequences, which have been curated by domain experts to ensure high standards of accuracy and completeness.
		ISD tools for management of influenza viral sequences and study of the molecular evolution of the influenza virus are designed to expedite the typical tasks of molecular epidemiology.
		Notice to Users: Please cite the Influenza Sequence Database (ISD) in your publications as follows: Macken, C., Lu, H., Goodman, J., and Boykin, L., "The value of a database in surveillance and vaccine selection." in Options for the Control of Influenza IV.
	www.flu.lanl.gov (458 words)

	GenBank Database
		GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.
		GenBank is part of the International Nucleotide Sequence Database Collaboration, which is comprised of the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the National Center for Biotechnology Information.
		Most sequence analysis programs on PSC supercomputers are capable of reading in GenBank data in the GenBank flat file format.
	www.psc.edu /general/software/packages/genbank/genbank.html (281 words)

	ITMI Triticeae Repeat Sequence Database
		Web ResourcesBesides the Database, the GrainGenes Website includes a large array of other data resources, classified by topic here.
		Database Information How to join the grains mailgroup.
		GrainGenes is a product of the Agricultural Research Service of the US Department of Agriculture.
	wheat.pw.usda.gov /ITMI/Repeats/index.shtml (170 words)

	Genome Projects - The Institute for Genomic Research (Site not responding. Last check: 2007-10-03)
		TIGR's Genome Projects are a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans.
		Containing the complete set of sequence reads, quality values, and ancillary data for selected genome projects, for use in comparing assemblers or polymorphism studies.
		Integrating data from international EST sequencing and gene research projects, the Gene Indices are an analysis of the transcribed sequences represented in the world's public EST data.
	www.tigr.org /tdb/index.shtml (391 words)

	HIV Databases
		The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials.
		This project is funded by the Division of AIDS of the National Institute of Allergy and Infectious Diseases (NIAID), a part of the National Institutes of Health (NIH).
		Previously this would select all sequences associated with a patient, and then retain only one sequence for each patient; sequences without patient information were not selected.
	hiv-web.lanl.gov /index.html (419 words)

	Hepatitis C Virus Databases
		The Hepatitis C Virus (HCV) Database Project is funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID).
		The HCV database group strives to present HCV-associated genetic and immunologic data in a userfriendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.
		This project is deeply indebted to the HIV Database Group, led by Dr. Bette Korber, for much of its tools, infrastructure and philosophy; the two databases continue to collaborate closely and to share software and resources.
	hcv.lanl.gov (210 words)

Try your search on: Qwika (all wikis)