infobox biodatabase title The Ensembl genome database project. logo File Ensembl release58 sgcb screenshot.png 300px description Ensembl scope organism center Wellcome Trust Sanger Institute br European ... frequency curation bookmark version Ensembl is a joint scientific project between the European Bioinformatics ... P, Amode MR, Barrell D, et al. title Ensembl 2011 journal Nucleic Acids Res volume 39 issue Database ... B, et al. title Ensembl s 10th year journal Nucleic Acids Res. volume 38 issue Database issue pages D557 62 year 2010 month January pmid 19906699 pmc 2808936 doi 10.1093 nar gkp972 url ref , Ensembl ... researchers studying the genome s of our own species and other vertebrate s and model organism s. Ensembl ... matching of protein to DNA . In the Ensembl project, sequence data is fed into a software pipeline ... for subsequent analysis and display. Ensembl makes these data freely accessible to the world research community. All the data and code produced by the Ensembl project is available to download, and there is also a publicly accessible database server allowing remote access. In addition, the Ensembl ... variation s and regulatory features. Since April 2009, a sister project, Ensembl Genomes , has extended the scope of Ensembl into invertebrate metazoa , plants , fungi , bacteria and protists , whilst the original project continues to focus on vertebrates. Displaying genomic data Image Ensembl release58 sgcb screenshot.png thumb Gene SGCB aligned to the human genome Central to the Ensembl concept ... Perl graphics display library. Alternative access methods In addition its website, Ensembl ..., Clamp M, and Birney E title The Ensembl Core Software Libraries journal Genome Research volume 14 ... data . The Ensembl website provides extensive information on http www.ensembl.org info docs api index.html ... References reflist 3 External links http www.ensembl.org Ensembl http vega.sanger.ac.uk Vega http pre.ensembl.org Pre Ensembl http www.ensemblgenomes.org Ensembl genomes http genome.ucsc.edu UCSC Genome ... more details
infobox biodatabase title Ensembl Genomes logo description An integrative resource for genome scale data from non vertebrate species. scope genomic organism pan center European Bioinformatics Institute laboratory author pmid Kersey & al. 2012 ref name kersey released 2009 standard format url http ensemblgenomes.org download webservice sql sparql webapp standalone license versioning frequency 4 5 times per year curation bookmark version 12 Ensembl Genomes is a scientific project to provide genome scale data from non vertebrate species ref name kersey PMID 22067447 ref . The project is run by the European Bioinformatics Institute , and was launched in 2009 using the Ensembl technology ref PMID 19033362 ref . Current species 249 bacteria http bacteria.ensembl.org , including Bacillus , Borrelia , Buchnera bacterium Buchnera , and Mycobacterium . 14 protist s http protists.ensembl.org 34 metazoa http metazoa.ensembl.org 15 plant s http plants.ensembl.org 23 fungus fungi http fungi.ensembl.org See also Ensembl List of sequenced eukaryotic genomes Sequence analysis References reflist 2 External links http www.ensemblgenomes.org Ensembl genomes http www.ensembl.org Ensembl Wellcome Trust Category Bioinformatics Category Biological databases Category Wellcome Trust ... more details
PupaSuite is an interactive web based Single nucleotide polymorphism SNP analysis tool that allows for the selection of relevant SNPs within a gene , based on different characteristics of the SNP itself, such as validation status, type, frequency population data and putative functional properties pathological SNPs, SNPs disrupting potential transcription factor binding sites, intron exon boundaries... . Also, PupaSuite provides information about LD parameters based on genotype data from HapMap and identifies haplotype blocks and tag SNPs using the http www.broad.mit.edu mpg haploview Haploview program . PupaSuite operates with a collection of entries of dbSNP mapped to the Golden Path genome assembly , as implemented in human section of Ensembl http nar.oxfordjournals.org cgi content full 33 suppl 1 D447 Hubbard T. et al., 2005 . See also Bioinformatics biologically inspired computing Ensembl External links http pupasuite.bioinfo.cipf.es PupaSuite Category Bioinformatics software ... more details
Orphan date April 2012 noinclude This table of client computing client application software application s for the Distributed Annotation System has been created primarily for inclusion in its Distributed Annotation System parent page . The parent page puts the table in context, and you should go there for more information. The table is provided in a separate page so that it can be transcluded where necessary. Table follows noinclude class wikitable Name Description Links BioJava DAS Client Dasty A web client for visualizing protein sequence feature information using DAS http www.ebi.ac.uk dasty http www.ebi.ac.uk das srv uniprot dasty index.jsp?id Q24488 DasView A server side Perl application. This tool is mentioned in the original DAS publication, but has subsequently disappeared. EnsEMBL The EnsEMBL Genome Browser. Provides built in support for DAS http www.ensembl.org Geodesic An stand alone Java application http www.biodas.org geodesic Integrated Genome Browser IGB The Integrated Genome Browser IGB, pronounced ig bee is an application built upon the GenoViz SDK and Genometry for visualization and exploration of genomes and corresponding annotations from multiple data sources http genoviz.sourceforge.net Jalview A multiple sequence alignment editor & viewer http www.jalview.org OmniGene The user interface is based on the EnsEMBL interface http omnigene.sourceforge.net http sourceforge.net projects omnigene SPICE A browser for the annotations for protein sequences and structures http www.efamily.org.uk software dasclients spice http www.spice 3d.org http www.spice 3d.org dasobert STRAP Underlining sequence features in multiple alignments. Example output http www.charite.de bioinf strap exampleOutput.html http 3d alignment.eu The Institute for Genomic Research TIGR DAS Viewer http www.tigr.org tdb DAS dasview.html ? WormBase The WormBase genome Browser. Includes a DAS viewer named DASView includeonly small Edit this table small includeonly Category Bioinformatics ... more details
The International Protein Index IPI ref name IPIref cite journal author Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R title The International Protein Index an integrated database for proteomics experiments journal Proteomics volume 4 issue 7 pages 1985 8 year 2004 month July pmid 15221759 doi 10.1002 pmic.200300721 url ref is database that was created to give the proteomics community a resource that enables Accession number bioinformatics accession numbers from a variety of bioinformatics databases to be mapped a complete set of proteins for a species i.e. a reference set IPI was launched in 2001 by the European Bioinformatics Institute EBI when databases cataloguing human genes varied greatly and had few links between them. Since then much more data has been produced giving a more complete picture and databases have collaborated to synchronize data. Currently many model organisms have a reference set of genes proteins which are catalogued in Ensembl UniProt respectively, as well as other species specific databases. Retirement Due to advances in data organization the need for IPI is diminishing. Citation needed date June 2011 The EBI has announced that this service will be closing when appropriate and has advised users of its services to employ UniProtKB accession numbers as their protein identifiers. References Reflist External links http www.ebi.ac.uk IPI IPIhelp.html IPI EBI http www.ensembl.org index.html Ensembl http www.ebi.ac.uk European Bioinformatics Institute http www.uniprot.org UniProt Category Biological databases Category Bioinformatics Category Proteomics Category Databases in the United Kingdom Category Indexes Category Indexing Category Data synchronization ... more details
Ensembl Resources User Manual author DECIPHER consortium date 28 February 2010 work publisher Wellcome ... and Phenotype in Humans using Ensembl Resources , DECIPHER was initiated in 2004 at the Wellcome ... for clinicians and researchers linking genomic microarray data with phenotype using the Ensembl genome ... as are imprinted gene s. ref and view the region in the Ensembl genome browser to see ... through Ensembl if a Informed consent consent form is signed by the patient. ref name flow With informed ... consented anonymized patient data in DECIPHER and Ensembl, without the identity of the submitting ... http ncbi36.ensembl.org Homo sapiens Info Index Human Ensembl Wellcome Trust Category Biological ... more details
protein Name Androgen binding protein, Sex hormone binding globulin caption image width HGNCid 10839 Symbol SHBG AltSymbols ABP EntrezGene 6462 OMIM 182205 RefSeq NM 001040 UniProt P04278 PDB ECnumber Chromosome 17 Arm p Band 13 LocusSupplementaryData p12 Androgen binding protein ABP is a glycoprotein beta globulin produced by the Sertoli cells in the seminiferous tubules of the testis that binds specifically to testosterone T , dihydrotestosterone DHT , and 17 beta estradiol . Because ABP binds to T and DHT, these hormones are made less lipophilic and become concentrated within the luminal fluid of the seminiferous tubules. The higher levels of these hormones enable spermatogenesis in the seminiferous tubules and sperm maturation in the epididymis . ABP has the same amino acid sequence as sex hormone binding globulin SHBG the difference is the site of production and the addition of different sugar moieties. ABP contains 403 amino acids, resulting in a molecular weight of 44,533. Its gene is located on chromosome 17 . ABP s production is regulated under influence of Follicle stimulating hormone FSH on Sertoli cell, enhanced by insulin , retinol , and testosterone . ABP may also be secreted in other organs for instance, mice produce a saliva ry ABP. See also Sex hormone binding globulin SHBG References Ensembl ENSG00000129214 External links MeshName Androgen Binding Protein Carrier proteins Category Glycoproteins de Androgen bindendes Protein pt Prote na ligadora de andr genos ... more details
The Distributed Annotation System DAS is an open source project that is used in bioinformatics to share and collate genomic annotation information. ref name pmid11667947 cite journal doi 10.1186 1471 2105 2 7 author Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L title The distributed annotation system. journal BMC Bioinformatics volume 2 pages 7 year 2001 pmid 11667947 pmc 58584 ref ref name pmid17237073 cite journal author Finn RD, Stalker JW, Jackson DK, Kulesha E, Clements J, Pettett R title ProServer a simple, extensible Perl DAS server. journal Bioinformatics volume 23 issue 12 pages 1568 70 year 2007 pmid 17237073 pmc 2989875 doi 10.1093 bioinformatics btl650 ref ref name pmid18673527 cite journal author Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, K h ri A, Kulesha E, Mac as JR, Reeves GA, Prlic A title Integrating biological data the Distributed Annotation System. series 9 journal BMC Bioinformatics volume Suppl 8 pages S3 year 2008 pmid 18673527 doi 10.1186 1471 2105 9 S8 S3 pmc 2500094 ref It first originated as the work of Robin Dowell, Rodney Jokerst, Allen Day, Sean Eddy and Lincoln Stein , ref name pmid11667947 but it has since evolved into a community driven project with its main hub http www.biodas.org BioDAS . The current stable version of DAS is 2.0, which is also written as DAS 2 , whereas the older but still commonly used version 1.6 is abbreviated as DAS 1 . The latter DAS 2 specification is not compatible with DAS 1. ref name das2 http www.biodas.org wiki DAS 2 The DAS 2 Protocol ref Sites and tools currently using DAS http www.dasregistry.org The DAS registration server http www.ensembl.org Ensembl The Ensembl Genome Browser http genome.ucsc.edu UCSC Genome Browser http www.wormbase.org WormBase http www.flybase.org FlyBase http www.jcvi.org TIGR http www.sanger.ac.uk proserver ProServer http supfam.org SUPERFAMILY SUPERFAMILY http www.ebi.ac.uk interpro InterPro DAS clients ... more details
PBB geneid 57094 GNF Protein box Name Carboxypeptidase A6 image image source PDB HGNCid 17245 MGIid Symbol AltSymbols CPA6 CBPA6 CPAH OMIM 609562 ECnumber 3.4.17.1 Homologene 75130 GeneAtlas image1 GeneAtlas image2 GeneAtlas image3 Protein domain image Function GNF GO id GO 0004181 text metallocarboxypeptidase activity GNF GO id GO 0008233 text peptidase activity GNF GO id GO 0008237 text metallopeptidase activity GNF GO id GO 0008270 text zinc ion binding GNF GO id GO 0046872 text metal ion binding Component GNF GO id GO 0005576 text extracellular region GNF GO id GO 0005578 text proteinaceous extracellular matrix Process GNF GO id GO 0006508 text proteolysis Hs EntrezGene 57094 Hs Ensembl ENSG00000165078 Hs RefseqmRNA Hs RefseqProtein NP 065094.3 Hs GenLoc db hg19 Hs GenLoc chr 8 Hs GenLoc start 68334360 Hs GenLoc end 68658620 Hs Uniprot Q8N4T0 Mm EntrezGene 329093 Mm Ensembl ENSMUSG00000042501 Mm RefseqmRNA NM 177834.3 Mm RefseqProtein NP 808502.2 Mm GenLoc db mm9 Mm GenLoc chr 1 Mm GenLoc start 10314801 Mm GenLoc end 10710026 Mm Uniprot Q5U901 path PBB 57094 Carboxypeptidase A6 CPA6 is an metallocarboxypeptidase enzyme that in humans is encoded by the CPA6 gene . ref name entrez cite web title Entrez Gene Carboxypeptidase A6 url http www.ncbi.nlm.nih.gov sites entrez?db gene&cmd retrieve&list uids 57094 accessdate 2011 11 25T03 01 34.724 08 00 ref It is highly expressed in the adult mouse olfactory bulb and is broadly expressed in the embryo nic brain and other tissues. ref name pmid18178555 cite journal author Lyons PJ, Callaway MB, Fricker LD title Characterization of carboxypeptidase A6, an extracellular matrix peptidase journal The Journal of Biological Chemistry volume 283 issue 11 pages 7054 63 year 2008 month March pmid 18178555 doi 10.1074 jbc.M707680200 url http www.jbc.org cgi pmidlookup?view long&pmid 18178555 ref The protein encoded by this gene belongs to the family of carboxypeptidase s, which catalyze the release of C terminus C terminal amino aci ... more details
http racerx00.tamu.edu bee resources.html BeeBase is an online bioinformatics database that displays data related to Apis mellifera , the European honey bee. It was developed in collaboration with the Honey Bee Genome Sequencing Consortium . In Feb 2007, BeeBase consisted of a http gmod.org wiki GBrowse GBrowse based genome viewer and a http gmod.org wiki CMap CMap based comparative map viewer, both modules of the Generic Model Organism Database GMOD project. The genome viewer included tracks for known honey bee genes, predicted gene sets Ensembl, NCBI, EMBL Heidelberg , STS markers Solignac and Hunt linkage maps , honey bee expressed sequence tags ESTs , homologs in Drosophila melanogaster fruit fly , mosquito and other insects and transposable element s. The honey bee comparative map viewer displayed linkage maps and the physical map genome assembly , highlighting markers that are common among maps. Future enhancements planned for BeeBase are a QTL viewer and a gene expression database. The genome sequence will serve as a reference to link these diverse data types. Biological data and services available on BeeBase include DNA and protein sequence data official bee gene set developed by and hosted at Beebase genome browser linkage maps server to search the honey bee genome using BLAST Beebase organized the community annotation of the bee genome in collaboration with Baylor College of Medicine Human Genome Sequencing Center http www.genome.org cgi content full 16 11 1329 . In the United Kingdom the National Bee Unit, part of the Food and Environment Research Agency, independently runs an information website under the name BeeBase https secure.fera.defra.gov.uk beebase . Category Model organism databases Category Genome projects Category Beekeeping bee stub ... more details
Plant ontology PO is a set of controlled vocabularies ontology ontologies , developed by the Plant Ontology Consortium . These ontologies describe plant structures and growth and developmental stages, providing a semantic framework for cross species queries across databases. Project Members New York Botanical Garden L. H. Bailey Hortorium at Cornell University Oregon State University Ensembl SoyBase SSWAP SGN Gramene The Arabidopsis Information Resource TAIR MaizeGDB University of Missouri at St. Louis Missouri Botanical Garden See also Generic Model Organism Database Open Biomedical Ontologies http obofoundry.org OBO Foundry References Plant Structure Ontology PSO A morphological and anatomical ontology of flowering plants. http www.springer.com computer computational biology and bioinformatics book 978 1 84628 884 5 In Anatomy Ontologies for Bioinformatics, Springer, 2008, p 27 42 The Plant Ontology Database a community resource for plant structure and development stages controlled vocabulary and annotations. http nar.oxfordjournals.org cgi content full 36 suppl 1 D449 Nucleic Acid Research, 2008, 36 Database issue D449 D454 The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. http www.plantphysiol.org cgi content full 143 2 587 Plant Physiology,2007, 143 587 599 Whole plant growth stage ontology for angiosperms and its application in plant biology. http www.plantphysiol.org cgi content full 142 2 414 Plant Physiology, 2006,142 414 428 Plant Ontology PO a controlled vocabulary of plant structures and growth stages. http www.hindawi.com GetPDF.aspx?doi 10.1002 cfg.496 Comparative and Functional Genomics, 2005, Volume 6 7 8 , 388 397 The Plant Ontology Consortium and Plant Ontologies. http onlinelibrary.wiley.com doi 10.1002 cfg.154 full Comparative and Functional Genomics, 2002, Vol 3 2 , 137 142 External links http www.plantontology.org Plant Ontology Consortium http www.gramene.org Gramene http www.Arabidopsis.org TAI ... more details
The Vertebrate and Genome Annotation Vega project provides manual curation of vertebrate genomes for the scientific community. ref cite journal author Ashurst JL, Chen CK, Gilbert JG, et al. title The Vertebrate Genome Annotation Vega database journal Nucleic Acids Research volume 33 issue Database issue pages D459 65 year 2005 month January pmid 15608237 pmc 540089 doi 10.1093 nar gki135 ref The Vega data repository is publicly available, regularly updated and includes Genome project Genome annotation annotations of several finished vertebrate genome sequences. ref cite journal author Loveland J title VEGA, the genome browser with a difference journal Briefings in Bioinformatics volume 6 issue 2 pages 189 93 year 2005 month June pmid 15975227 doi 10.1093 bib 6.2.189 ref Human, mouse and zebrafish are in the process of being completely annotated, whereas for other species the annotation is only of specific genomic regions of particular biological interest ref http vega.sanger.ac.uk Vega website homepage, retrieved 2012 02 21 ref . The Vega website is built upon the Ensembl codebase. ref cite journal author Searle SM, Gilbert J, Iyer V, Clamp M title The otter annotation system journal Genome Research volume 14 issue 5 pages 963 70 year 2004 month May pmid 15123593 pmc 479127 doi 10.1101 gr.1864804 ref The Vega database is run and developed by the Wellcome Trust Sanger Institute . References reflist External links http vega.sanger.ac.uk Vega homepage Category Bioinformatics Category Biological databases bioinformatics stub ... more details
GNF Protein box Name Transmembrane protein 229b image image source PDB HGNCid 20130 MGIid Symbol TMEM229b AltSymbols OMIM ECnumber Homologene GeneAtlas image Function NotAProtein Orthologs Hs EntrezGene 161145 Hs Ensembl Hs RefseqmRNA NM 182526.2 Hs RefseqProtein NP 872332.1 Hs GenLoc db Hs GenLoc chr 14q24.1 Hs GenLoc start 67936983 Hs GenLoc end 67982021 Hs Uniprot Mm EntrezGene Mm Ensembl Mm RefseqmRNA NM 001170401.1 Mm RefseqProtein NP 001163872.1 Mm GenLoc db mm9 Mm GenLoc chr 12 Mm GenLoc start 80062782 Mm GenLoc end 80108614 Mm Uniprot Path 268567 IUPHAR Transmembrane protein 229b is a human transmembrane protein protein encoded a gene called TMEM229b. ref name Genecards cite web title TMEM229B Gene GeneCards T229B Protein T229B Antibody. url http www.genecards.org cgi bin carddisp.pl?gene TMEM229B&search TMEM229B work GeneCards V3 Human Genes Gene Database accessdate 2011 04 19 ref Features of the TMEM229B gene The TMEM229B gene is located on the sense strand of chromosome 14 at location 14q24.1 and spans the chromosomal locus 67,936,983 67,982,021. ref name Ensembl cite web title Gene TMEM229B ENSG00000198133 url http useast.ensembl.org Homo sapiens Gene Summary?g ENSG00000198133 r 14 67936983 67982021 t ENST00000357461 work The Ensembl Project publisher European Bioinformatics Institute, European Molecular Biology Laboratory, and Wellcome Trust Sanger Institute accessdate 2011 04 19 ref Covering a total of 45,038 base pairs bp along the chromosome, the TMEM229B gene has a total of 3 exons in its primary unspliced transcript mRNA of 4,068 bp. There are a total of 7 transcript variants for TMEM229B ranging in mRNA size from 519 bp to 5008 bp. ref name AceView cite web title AceView synopsis of TMEM229B url http www.ncbi.nlm.nih.gov work AceView accessdate 24 April 2011 ref The TMEM229B gene is flanked by phosphatidylinotisol glycan anchor class H PIGH , a protein associated with the endoplasmic reticulum specifically GPI anchor biosynthesis, and PLEK2 on its ... more details
ref ref cite pmid 12727907 ref notable students known for Ensembl , ref cite pmid 11752248 ref ... used Ensembl genome browser, and highly cited ref http scholar.google.com scholar?q ewan birney ... community. Perhaps even more important to biology is his leadership of the Ensembl genome annotation ... work co leading the Ensembl project has made high quality genome annotation available freely over the web ... accessible and easily available for mining. The Ensembl project has been open source from the outset ... more details
at several locations, using dedicated browsers such as Ensembl or UCSC Genome Browser . ref name ensembl cite journal author Flicek P, Aken BL, Beal K, et al. title Ensembl 2008 journal Nucleic Acids ... more details
Multiple issues cleanup rewrite February 2009 expert subject February 2009 orphan February 2009 The PBB Controls template provides controls for Protein Box Bot, please see Template PBB Controls for details. The IPC Protein box is automatically maintained by iPC s Protein Box Bot. See Template PBB Controls to Stop updates. IPC Protein box image image source PDB Name GA Insensitive HGNCid Symbol GAI AltSymbols AT1G14920 F10B6.34 F10B6 34 GA INSENSITIVE GAI PROTEIN RESTORATION ON GROWTH ON AMMONIA RGA2 OMIM ECnumber Homologene MGIid GeneModel image1 AT1G14920 GeneModel image1.png GeneAtlas image1 Function GNF GO id GO 0003700 text transcription factor activity Component GNF GO id GO 0005634 text nucleus Process GNF GO id GO 0042538 text hyperosmotic salinity response GNF GO id GO 0009938 text negative regulation of gibberellic acid mediated signaling GNF GO id GO 0010187 text negative regulation of seed germination GNF GO id GO 0010187 text negative regulation of seed germination Orthologs IPC Ortholog box Athal EntrezGene 838057 Athal Ensembl Athal RefseqProtein NP 172945 Athal RefseqmRNA NM 101361 Athal GenLoc db arabidopsis Athal GenLoc chr 1 Athal GenLoc start 5149221 Athal GenLoc end 5151349 Athal Uniprot Q9LQT8 Osat EntrezGene Osat Ensembl Osat RefseqmRNA Osat RefseqProtein Osat GenLoc db Osat GenLoc chr Osat GenLoc start Osat GenLoc end Osat Uniprot In the vocabulary of gene identification, GAI , also known as GA INSENSITIVE , is an http species.wikimedia.org wiki Arabidopsis thaliana Arabidopsis thaliana gene . ref name entrez cite web title Entrez Gene GAI url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 838057 accessdate ref The PBB Summary template is automatically maintained by Protein Box Bot. See Template PBB Controls to Stop updates. IPC Summary section title summary text Similar to a putative transcription factor and transcriptional coactivators. Repressor of GA responses and involved in gibberellic acid mediated signal ... more details
Orphan date February 2009 InterMine is a powerful open source data warehouse system. Using InterMine, you can create databases of biological data accessed by sophisticated web query tools. InterMine can be used to create databases from a single data set or can integrate multiple sources of data. Support is provided for several common biological formats and there is a framework for adding your own data. InterMine includes an attractive, user friendly web interface that works out of the box and can be easily customised for your specific needs. ref http www.intermine.org ref InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the sequence ontology and supports several biological data formats, just configure which organisms or data files are required. It is easy to extend the data model and integrate your own data, Java and Perl APIs and an XML format to help import custom data. Supported data formats Generic Model Organism Database Chado database schema Chado GFF GFF3 FASTA Gene Ontology GO & gene association files UniProt XML PSI XML protein interactions, Protein Structure Initiative InParanoid orthologs Ensembl Web application A web application allows creation of custom queries, includes template queries web forms to run canned queries and can upload and operate on lists of data. It is possible to configure create widgets to analyse lists with graphs and enrichment statistics. An admin user can publish new template queries, change report pages and create public lists at any time without any programming. Many aspects of the web app can be configured and branded. Current projects not exhaustive list Generic Model Organism Database http www.modencode.org modENCODE http www.flymine.org FlyMine http www.metabolicmine.org metabolicMine http ratmine.mcw.edu RatMine http yeastmine.yeastgenome.org YeastMine http targetmine.nibio.go.jp TargetMine http mitominer.mrc mbu.cam.ac.uk MitoMiner http zmine.zfin.or ... more details
Pairwise Algorithm ref cite journal last E first Birney title PairWise and SearchWise Finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames journal Nucleic Acids year 1996 volume 24 issue 14 ref is a dynamic alignment algorithm which compares a protein profile a residue scoring matrix for one or more aligned sequences against the three translation frames of a DNA strand, allowing frameshifting. The most remarkable feature of PairWise as compared to other Protein DNA alignment tools is that PairWise allows frameshifting during alignment. History PairWise was generated by Ewan Birney when he is an undergraduate in Oxford.Birney has generated a series of algorithm in his career. The significant ones include PairWise, SearchWise, GeneWise, GenomeWise and Ensembl . Among these algorithms, PairWise is the earliest one, and it s also the foundation of other three Wise algorithms. Frameshifting refers to the phenomena where in one DNA strands, there are more than one translation frame. For normal Protein DNA alignment tools, they first choose one of three frame DNA frames to translate the DNA into a protein sequence , and then compare it with the given protein. Such alignment is based on the assumption that the DNA translation frame is not interrupted for the whole DNA strand. However, this is not generally true. The PairWise algorithm is a variant of the Smith Waterman best local alignment algorithm. These algorithms all belong to the class known as minimal string edit algorithms. The main differences between PairWise and other alignment algorithm is that, besides normal penalties such as Gap Opening Penalty GOP , Gap Extension Penalty GEP and Match, PairWise introduced two new penalties called Frame Opening Penalty FOP and Frame Extension Penalty FEP , which will be incurred when a frameshift is accepted and extended respectively. Illustration Figure 1 illustrates the alignment result when one protein sequence a ... more details
Genome Browser , and Ensembl . Statistical tests, specifically designed to handling count ... are further analyzed and their effect on transcripts is described similar to the Ensembl SNP Effect ... more details
GNF Protein box image image source PDB 1V65, 2YTF Name Zinc finger protein 184 HGNCid 12975 Symbol ZNF184 AltSymbols OMIM 602277 ECnumber Homologene 113602 MGIid 1922244 Protein domain image GeneAtlas image1 GeneAtlas image2 GeneAtlas image3 Function GNF GO id GO 0046872 text metal ion binding GNF GO id GO 0003677 text DNA binding GNF GO id GO 0008270 text zinc ion binding GNF GO id GO 0003676 text nucleic acid binding Component GNF GO id GO 0005634 text nucleus GNF GO id GO 0005622 text intracellular GNF GO id GO 0005737 text cytoplasm Process GNF GO id GO 0006355 text regulation of transcription, DNA dependent GNF GO id GO 0006350 text transcription Hs EntrezGene 7738 Hs Ensembl ENSG00000096654 Hs RefseqProtein NP 009080 Hs RefseqmRNA NM 007149 Hs GenLoc db hg18 Hs GenLoc chr 6 Hs GenLoc start 27418521 Hs GenLoc end 27440897 Hs Uniprot Q99676 Mm EntrezGene 193452 Mm Ensembl ENSMUSG00000006720 Mm RefseqmRNA NM 183014 Mm RefseqProtein NP 898835 Mm GenLoc db mm8 Mm GenLoc chr 13 Mm GenLoc start 22036963 Mm GenLoc end 22052648 Mm Uniprot PBB geneid 7738 Zinc finger protein 184 , also known as ZNF184 , is a protein that in humans is encoded by the ZNF184 gene ref name entrez cite web title Entrez Gene zinc finger protein 184 url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 7738 accessdate ref on chromosome 6. It was first identified by Goldwurm et al. in 1996. ref name goldwurm cite journal author Goldwurm S, Menzies ML, Banyer JL, Powell LW, Jazwinska EC title Identification of a novel Krueppel related zinc finger gene ZNF184 mapping to 6p21.3. journal Genomics volume 40 issue 3 pages 486 9 date 1997 03 15 pmid 9073517 doi 10.1006 geno.1996.4583 ref The National Center for Biotechnology Information NCBI Gene database entry ref name entrez for ZNF184 identifies conserved domains KRAB A Kr ppel associated box near the N terminus and Zn finger Zinc finger at the C terminus of the expressed protein. The former is associated with transcrip ... more details
WGAViewer ref cite journal author Ge D, Zhang K, Need AC, et al. title WGAViewer software for genomic annotation of whole genome association studies. journal Genome Research year 2008 volume 18 pages 640 643 doi 10.1101 gr.071571.107 pmid 18256235 issue 4 pmc 2279251 ref is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study GWAS . Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium LD with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP. Introduction Functions WGAViewer currently offers several classes of annotation of the GWAS results 1 Overview of WGA results allowing zooming in out searching for gene SNP top hits sorting with individual SNP annotation 2 Genic annotation of WGA results with explicit reference to align results with the latest genome build gene transcripts context ref cite journal author Hubbard TJ, Aken BL, Beal K, et al. title Ensembl 2007. journal Nucleic Acids Res. year 2007 volume 35 pages D610 7 doi 10.1093 nar gkl996 pmid 17148474 issue Database issue pmc 1761443 ref linkage disequilibrium context ref cite journal author The International HapMap Consortium title A second generation human haplotype map of over 3.1 million SNPs. journal Nature year 2007 volume 449 pages 851 61 doi 10.1038 nature06258 pmid 17943122 issue 7164 pmc 2689609 ref 3 Annotation for SNPs LD score for all HapMap SNPs in specified region association with specified gene expression ref cite journal author Stranger BE, Forrest MS, Clark AG, et al. title Genome wide associations of gene expression variation in humans. journal PLoS Genet. year 2005 volume 1 pages e78 doi 10.1371 journal.pgen.0010078 pmid 16362079 issue 6 pmc 1315281 ref SNP functio ... more details
annotations through their Subsystems approach. Other databases e.g. Ensembl rely on both curated .... ref cite web url http www.ensembl.org info about docs index.html title Ensembl s genome annotation ... ENCyclopedia Of DNA Elements ENCODE Entrez Gene Ensembl GENCODE Gene ontology Gene Ontology Consortium ... more details
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