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INFOBDGP: MATERIALS
About BDGP: general overview, contact information, news archive, how to cite BDGP The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center funded by the National Human Genome Research Institute and the National Institute of General Medical Sciences through its support of work in the Susan Celniker, J. Ben Brown, Erwin Frise and Gary KarpenBDGP: SEARCHES
Searches. Fly BLAST at FlyBase Compare your sequence to Drosophila melanogaster sequences, including genomic annotations, ESTs, published genes, flanking insertion sites and repeats. Analysis Tools Pattern Search, Genie, cis-analyst, Target Explorer, Promoter Prediction, Splice Site Prediction, Genotator, and other tools. BDGP: SPLICE SITE PREDICTION BY NEURAL NETWORK Training set: Our training and test sets of human and Drosophila melanogaster splice sites are available to the community for testing splice site predictors. They can be obtained from our collection of representative, standardized data sets of human and D. melanogaster genes. Publication: Reese MG, Eeckman, FH, Kulp, D, Haussler, D, 1997 BDGP: DROSOPHILA GENE COLLECTION Drosophila Gene Collection. DGC Release 1.0; After careful analysis of over 80,000 ESTs to find full-length cDNA clones, including verification of the 3' ends of these clones, we have selected 5,849 non-redundant cDNA clones for single colony purification and re-arraying (see What is the Drosophila Gene Collection? for more information). This is not a complete set of genes for the Drosophila BDGP: NEURAL NETWORK PROMOTER PREDICTION Publications: Reese MG, 2001. ``Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome'', Comput Chem 26 (1) ,51-6. Reese MG, 2000. ``Computational prediction of gene structure and regulation in the genome of Drosophila melanogaster '', PhD Thesis (PDF), UC Berkeley/Universityof Hohenheim.
BDGP: NEURAL NETWORK PROMOTER PREDICTION About the neural network method. NNPP is a method that finds eukaryotic and prokaryotic promoters in a DNA sequence. The function of the promoter as a initiator for transcription is one of the most complex processes in molecular biology. It has been shown that multiple functional sites in the primary DNA are involved in thepolymerase binding
BDGP: EXPRESSION VECTORS BDGP Resources Donor Vectors. We use the pDNR-Dual vector and Clontech's In-Fusion PCR Cloning System to generate the ExpressR-NS and ExpressR-O clones. The important features of pDNR-Dual are the placement of multiple-cloning sites (MCS), a splice donor sequence, a 6xHN tag, and a selectable marker (a promotor-less chloramphenicol resistance gene) between two flanking loxP sites. BDGP: NEURAL NETWORK PROMOTER PREDICTION: ABSTRACT With the TDNN, we achieve very good prediction accuracy for the local core promoter features, which is somewhat surprising given the non-local structure of the promoter site. The network predicts the 9 known promoters in the whole genome of the adeno2-virus with a false positive score of 2.5%. On a test set containing 42 known human geneBDGP: SPLICE: HELP
Splice sites are the key signal sequences that determine the boundaries of exons. A method for splice site detection should ideally be based on a thorough understanding of the complex eukaryotic splicing process. We trained a backpropagation feedforward neural network with one layer of hidden units to recognize 5' and 3' splicesites, using a
BDGP: POT2 VECTOR
BDGP Resources pOT2 Vector. The SP6 primer does not work well for sequencing, so we use the PM001 primer for 3' EST sequencing, and the T7 primer for 5' EST sequencing. BDGP: HOMEEST SEQUENCINGBDGP NEWS ARCHIVEMETAMORPHOSISCONTACTINFOBDGP: MATERIALS
About BDGP: general overview, contact information, news archive, how to cite BDGP The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center funded by the National Human Genome Research Institute and the National Institute of General Medical Sciences through its support of work in the Susan Celniker, J. Ben Brown, Erwin Frise and Gary KarpenBDGP: SEARCHES
Searches. Fly BLAST at FlyBase Compare your sequence to Drosophila melanogaster sequences, including genomic annotations, ESTs, published genes, flanking insertion sites and repeats. Analysis Tools Pattern Search, Genie, cis-analyst, Target Explorer, Promoter Prediction, Splice Site Prediction, Genotator, and other tools. BDGP: SPLICE SITE PREDICTION BY NEURAL NETWORK Training set: Our training and test sets of human and Drosophila melanogaster splice sites are available to the community for testing splice site predictors. They can be obtained from our collection of representative, standardized data sets of human and D. melanogaster genes. Publication: Reese MG, Eeckman, FH, Kulp, D, Haussler, D, 1997 BDGP: DROSOPHILA GENE COLLECTION Drosophila Gene Collection. DGC Release 1.0; After careful analysis of over 80,000 ESTs to find full-length cDNA clones, including verification of the 3' ends of these clones, we have selected 5,849 non-redundant cDNA clones for single colony purification and re-arraying (see What is the Drosophila Gene Collection? for more information). This is not a complete set of genes for the Drosophila BDGP: NEURAL NETWORK PROMOTER PREDICTION Publications: Reese MG, 2001. ``Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome'', Comput Chem 26 (1) ,51-6. Reese MG, 2000. ``Computational prediction of gene structure and regulation in the genome of Drosophila melanogaster '', PhD Thesis (PDF), UC Berkeley/Universityof Hohenheim.
BDGP: NEURAL NETWORK PROMOTER PREDICTION About the neural network method. NNPP is a method that finds eukaryotic and prokaryotic promoters in a DNA sequence. The function of the promoter as a initiator for transcription is one of the most complex processes in molecular biology. It has been shown that multiple functional sites in the primary DNA are involved in thepolymerase binding
BDGP: EXPRESSION VECTORS BDGP Resources Donor Vectors. We use the pDNR-Dual vector and Clontech's In-Fusion PCR Cloning System to generate the ExpressR-NS and ExpressR-O clones. The important features of pDNR-Dual are the placement of multiple-cloning sites (MCS), a splice donor sequence, a 6xHN tag, and a selectable marker (a promotor-less chloramphenicol resistance gene) between two flanking loxP sites. BDGP: NEURAL NETWORK PROMOTER PREDICTION: ABSTRACT With the TDNN, we achieve very good prediction accuracy for the local core promoter features, which is somewhat surprising given the non-local structure of the promoter site. The network predicts the 9 known promoters in the whole genome of the adeno2-virus with a false positive score of 2.5%. On a test set containing 42 known human geneBDGP: SPLICE: HELP
Splice sites are the key signal sequences that determine the boundaries of exons. A method for splice site detection should ideally be based on a thorough understanding of the complex eukaryotic splicing process. We trained a backpropagation feedforward neural network with one layer of hidden units to recognize 5' and 3' splicesites, using a
BDGP: POT2 VECTOR
BDGP Resources pOT2 Vector. The SP6 primer does not work well for sequencing, so we use the PM001 primer for 3' EST sequencing, and the T7 primer for 5' EST sequencing. BDGP: CDNA & EST PROJECTS cDNA & EST Projects. A description and update of the generation of expression-ready clone sets. A selection of non-redundant clones from over 10,000 full-insert sequenced cDNAs that can be utilized for proteomics and functional genomics. A description and information of clone sets that comprise the DGC. BDGP: CITING THE BDGP D. melanogaster Genome. Adams et al. Entries in GenBank databases can be cited in the same way you would cite any publication, giving the authors, date and accession number. In addition, genomic sequence should be cited as Celniker et al. 2002 Genome Biology 3:research0079.1-0079.14. Data on BAC and P1 clones: Data based on theBAC physical map
BDGP: REPRESENTATIVE BENCHMARK DATA SETS OF HUMAN DNA Projects Representative Benchmark Data Sets of Human DNA Sequences. Please bookmark this site and NOT the sites of the data it is pointing to! This site will serve as a stable interface to access the datasets, but the location of the sets will be subject to change.BDGP: SPLICE: HELP
Splice sites are the key signal sequences that determine the boundaries of exons. A method for splice site detection should ideally be based on a thorough understanding of the complex eukaryotic splicing process. We trained a backpropagation feedforward neural network with one layer of hidden units to recognize 5' and 3' splicesites, using a
BDGP: GENE DISRUPTION PROJECT Gene Disruption Project Database The GDP database of P-element, piggyBac and Minos lines from the ongoing GDP screen and all other mapped insertion lines from other labs that are available in the Bloomington Stock Center. P-Element Lethal Screen. The EP Controlled Misexpression Screen. Fly Stocks Order Drosophila transposon insertionstocks.
BDGP: LABS THAT RECEIVED THE DGCR1.0 The DGCr1.0 is available from BACPAC Resources, OpenBiosystems, or MRC geneservice. The following laboratories have received aliquots of the DGCr1.0 as 384-well bacterial stock plates or 96-well plasmid DNA plates. The US labs were chosen by the Drosophila Board. We do not know which of the US labs are distributing arrays of the DGC to otherlabs.
BDGP: POTB7 VECTOR
BDGP Resources pOTB7 Vector (Vector diagram drawn using PlasMapper).. The pOTB7 plasmid began with the pOT2A backbone. A 204bp fragment was designed to facilitate the use of the Gateway expression system from Life Technologies. Specifically: An attB1 site isBDGP: POT2 VECTOR
BDGP Resources pOT2 Vector. The SP6 primer does not work well for sequencing, so we use the PM001 primer for 3' EST sequencing, and the T7 primer for 5' EST sequencing. BDGP: INVERSE PCR & CYCLE SEQUENCING OF P ELEMENT Mix the following in 200 ul PCR tubes: Cycle Sequence in a Perkin-Elmer 9700 (~2.5 hours) 96° 10 sec./ 50° 5 sec./ 60° 4 min. cycle 25 times followed by 4° hold. To purify reactions add cold 70% EtOH, let stand 20 minutes at RT, centrifuge for 30 minutes, discardEtOH and dry.
BDGP: 2ND CHROMOSOME: SOURCE HOSKINS ET AL. STS Cytological location Flanking sequence Nucleotide position Oregon R Canton S w;iso2;iso3 P strain 1 Q1028 P strain 2 Release 1 y;cnbwsp RFLP? Dm0447: 21D1-21D2 BDGP: HOMEEST SEQUENCINGBDGP NEWS ARCHIVEMETAMORPHOSISCONTACTINFOBDGP: MATERIALS
About BDGP: general overview, contact information, news archive, how to cite BDGP The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center funded by the National Human Genome Research Institute and the National Institute of General Medical Sciences through its support of work in the Susan Celniker, J. Ben Brown, Erwin Frise and Gary KarpenBDGP: SEARCHES
Searches Searches. Fly BLAST at FlyBase Compare your sequence to Drosophila melanogaster sequences, including genomic annotations, ESTs, published genes, flanking insertion sites and repeats.; Genome Annotations at FlyBase; All Searches Flybase, BDGP ; Analysis Tools Pattern Search, Genie, cis-analyst, Target Explorer, Promoter Prediction, Splice Site Prediction, Genotator, and other tools. BDGP: SPLICE SITE PREDICTION BY NEURAL NETWORK Training set: Our training and test sets of human and Drosophila melanogaster splice sites are available to the community for testing splice site predictors. They can be obtained from our collection of representative, standardized data sets of human and D. melanogastergenes.
BDGP: DROSOPHILA GENE COLLECTION Drosophila Gene Collection. DGC Release 1.0; After careful analysis of over 80,000 ESTs to find full-length cDNA clones, including verification of the 3' ends of these clones, we have selected 5,849 non-redundant cDNA clones for single colony purification and re-arraying (see What is the Drosophila Gene Collection? for more information). This is not a complete set of genes for the Drosophila BDGP: NEURAL NETWORK PROMOTER PREDICTION Searches Neural Network Promoter Prediction. Read Abstract Help. PLEASE NOTE: This server runs the 1999 NNPP version 2.2 (March 1999) of the promoter predictor. Enter a DNA sequence to find possible transcription promoters BDGP: NEURAL NETWORK PROMOTER PREDICTION Searches Neural Network Promoter Prediction. Read Abstract. About the neural network method. NNPP is a method that finds eukaryotic and prokaryotic promoters in a DNA sequence. BDGP: EXPRESSION VECTORS BDGP Resources Donor Vectors. We use the pDNR-Dual vector and Clontech's In-Fusion PCR Cloning System to generate the ExpressR-NS and ExpressR-O clones. The important features of pDNR-Dual are the placement of multiple-cloning sites (MCS), a splice donor sequence, a 6xHN tag, and a selectable marker (a promotor-less chloramphenicol resistance gene) between two flanking loxP sites.BDGP: SPLICE: HELP
Searches Human and Drosophila melanogaster Splice Site Prediction using Neural Networks. Read Abstract. About the neural network method. Splice sites are the key signal sequences that determine the boundaries of exons. BDGP: NEURAL NETWORK PROMOTER PREDICTION: ABSTRACT Searches Neural Network Promoter Prediction: Abstract & References. Do Search. References: (1) Waibel, A. H., Hanazawa, T., Hinton, G. E., Shikano, K., Lang, K. J..BDGP: POT2 VECTOR
BDGP Resources pOT2 Vector. The SP6 primer does not work well for sequencing, so we use the PM001 primer for 3' EST sequencing, and the T7 primer for 5' EST sequencing. BDGP: HOMEEST SEQUENCINGBDGP NEWS ARCHIVEMETAMORPHOSISCONTACTINFOBDGP: MATERIALS
About BDGP: general overview, contact information, news archive, how to cite BDGP The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center funded by the National Human Genome Research Institute and the National Institute of General Medical Sciences through its support of work in the Susan Celniker, J. Ben Brown, Erwin Frise and Gary KarpenBDGP: SEARCHES
Searches Searches. Fly BLAST at FlyBase Compare your sequence to Drosophila melanogaster sequences, including genomic annotations, ESTs, published genes, flanking insertion sites and repeats.; Genome Annotations at FlyBase; All Searches Flybase, BDGP ; Analysis Tools Pattern Search, Genie, cis-analyst, Target Explorer, Promoter Prediction, Splice Site Prediction, Genotator, and other tools. BDGP: SPLICE SITE PREDICTION BY NEURAL NETWORK Training set: Our training and test sets of human and Drosophila melanogaster splice sites are available to the community for testing splice site predictors. They can be obtained from our collection of representative, standardized data sets of human and D. melanogastergenes.
BDGP: DROSOPHILA GENE COLLECTION Drosophila Gene Collection. DGC Release 1.0; After careful analysis of over 80,000 ESTs to find full-length cDNA clones, including verification of the 3' ends of these clones, we have selected 5,849 non-redundant cDNA clones for single colony purification and re-arraying (see What is the Drosophila Gene Collection? for more information). This is not a complete set of genes for the Drosophila BDGP: NEURAL NETWORK PROMOTER PREDICTION Searches Neural Network Promoter Prediction. Read Abstract Help. PLEASE NOTE: This server runs the 1999 NNPP version 2.2 (March 1999) of the promoter predictor. Enter a DNA sequence to find possible transcription promoters BDGP: NEURAL NETWORK PROMOTER PREDICTION Searches Neural Network Promoter Prediction. Read Abstract. About the neural network method. NNPP is a method that finds eukaryotic and prokaryotic promoters in a DNA sequence. BDGP: EXPRESSION VECTORS BDGP Resources Donor Vectors. We use the pDNR-Dual vector and Clontech's In-Fusion PCR Cloning System to generate the ExpressR-NS and ExpressR-O clones. The important features of pDNR-Dual are the placement of multiple-cloning sites (MCS), a splice donor sequence, a 6xHN tag, and a selectable marker (a promotor-less chloramphenicol resistance gene) between two flanking loxP sites.BDGP: SPLICE: HELP
Searches Human and Drosophila melanogaster Splice Site Prediction using Neural Networks. Read Abstract. About the neural network method. Splice sites are the key signal sequences that determine the boundaries of exons. BDGP: NEURAL NETWORK PROMOTER PREDICTION: ABSTRACT Searches Neural Network Promoter Prediction: Abstract & References. Do Search. References: (1) Waibel, A. H., Hanazawa, T., Hinton, G. E., Shikano, K., Lang, K. J..BDGP: POT2 VECTOR
BDGP Resources pOT2 Vector. The SP6 primer does not work well for sequencing, so we use the PM001 primer for 3' EST sequencing, and the T7 primer for 5' EST sequencing. BDGP: GENOMIC DNA SEQUENCING PROJECT Please send comments or questions about the web site to bdgp at fruitfly dot orgbdgp at fruitfly dot org BDGP: CDNA & EST PROJECTS cDNA & EST Projects. Universal Proteomics Resources; A description and update of the generation of expression-ready clone sets. DrosophilaGold Collection
BDGP: CITING THE BDGP Citing the BDGP. Much of the data from the BDGP that is available from this web site or other outlets has not been published in the traditional sense of peer-reviewed papers.BDGP: SPLICE: HELP
Searches Human and Drosophila melanogaster Splice Site Prediction using Neural Networks. Read Abstract. About the neural network method. Splice sites are the key signal sequences that determine the boundaries of exons. BDGP: GENE DISRUPTION PROJECT Projects Gene Disruption Project. Gene Disruption Project Database The GDP database of P-element, piggyBac and Minos lines from the ongoing GDP screen and all other mapped insertion lines from other labs that are available in the Bloomington Stock Center.; P-Element Lethal Screen; The EP Controlled Misexpression Screen BDGP: REPRESENTATIVE BENCHMARK DATA SETS OF HUMAN DNA Projects Representative Benchmark Data Sets of Human DNA Sequences. Please bookmark this site and NOT the sites of the data it is pointing to! This site will serve as a stable interface to access the datasets, but the location of the sets will be subject to change.BDGP: POTB7 VECTOR
BDGP Resources pOTB7 Vector (Vector diagram drawn using PlasMapper).. The pOTB7 plasmid began with the pOT2A backbone. A 204bp fragment was designed to facilitate the use of the Gateway expression system from Life Technologies. Specifically: An attB1 site isBDGP: SLIP SCREEN
Inverse-PCR Screen (SLIP) Directed Approach for Isolating cDNAs. Mapping of ESTs to gene annotations shows that there are 3,125 annotated protein-coding genes not yet represented in the DGC. BDGP: INVERSE PCR & CYCLE SEQUENCING OF P ELEMENT The Pry2/Pry1 combination has a higher annealing temperature than the Pry4/Pry1 and Pry4/Plw3-1 combinations, but the resulting PCR products do not allow sequencing directly off the 3' BDGP: 2ND CHROMOSOME: SOURCE HOSKINS ET AL. STS Cytological location Flanking sequence Nucleotide position Oregon R Canton S w;iso2;iso3 P strain 1 Q1028 P strain 2 Release 1 y;cnbwsp RFLP? Dm0447: 21D1-21D2 BERKELEY DROSOPHILA GENOME PROJECTHOME
BDGP NEWS
August 14, 2019: Congratulations to Ysabel David for winning the BestOverall Poster
for the 2019 Biotech Partners Internship Program! October 5, 2017: Drosophila gut microbe sequences: * Acetobacter tropicalis Oregon-R-modENCODE Strain BDGP1 * Lactobacillus plantarum Oregon-R modENCODE Strain BDGP2 * Enterococcus durans Oregon-R modENCODE strain BDGP3 * Bacillus kochii Oregon-R modENCODE strain BDGP4 * Acetobacter pomorum Oregon-R-modENCODE Strain BDGP5 October 2, 2017: 2017 Nobel Prize in Physiology or Medicine Congratulations to Jeffrey C. Hall, Michael Rosbash and Michael W. Young for winning this year's Nobel Prize! August 12, 2015: Lessons from modENCODE . Brown JB, Celniker SE. Annu Rev Genomics Hum Genet. 2015 Jun 26. July 28, 2014: RELEASE 6of the _D.
melanogaster_ genome sequence has been released! June 2014 The modENCODE Consortium . We have published a series of papers on functional annotation of the _D. melanogaster_ genome. See our contributions here.
Metamorphosis : The Artistic Impressionsof Pamela Lewis
PROJECTS
* GENOMIC SEQUENCING * _D. MELANOGASTER_ RELEASE 6 GENOME * NATURAL TRANSPOSABLE ELEMENTS* SNP MAP
* COMPARATIVE GENOMICS * TRANSCRIPT SEQUENCING* EST SEQUENCING
* DROSOPHILA GENE COLLECTION* _MODENCODE _
* DATA COORDINATING CENTER* THE TRANSCRIPTOME
* CHROMOSOMAL PROTEINS * DOWNLOAD MODENCODE DROSOPHILA TRANSCRIPTOME V2 EXPRESSION SCORES* GENE EXPRESSION
* EXPRESSION PATTERNSSystematic
determination of patterns of gene expression in _Drosophila_ embryogenesis by RNA _in situ_ * MAPEXPLORER Viewer for self-organizing maps.* CRM ANALYSIS
* GENE DISRUPTION PROJECT Insertion of single transposable elements to disrupt and manipulate Drosophilagenes
RESOURCES
* _FLY UNIVERSAL PROTEOMICS RESOURCE _ Search for _Drosophila_ clones for expression and tissue culture * _HUMAN UNIVERSAL PROTEOMICS RESOURCE _ Search for Human Gateway expression clones * DOWNLOAD Sequence data sets and annotations in fasta or xml format by http or ftp * MATERIALS Request genomic or cDNA clones, library filters or fly stocks, vector maps. * PUBLICATIONS Browse or download BDGPpapers
* METHODS BDGP laboratory protocolsSOFTWARE TOOLS
* ANALYSIS TOOLS Search sequences for CRMs, promoters, splice sites, and gene predictionsSEARCH BDGP SITE
* GO TO FLYBASE
------------------------- ABOUT BDGP: general overview , contact information , news archive , how tocite BDGP
The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center funded by the National Human Genome Research Institute and the National Institute of General Medical Sciences through its support of work in the Susan Celniker, J. Ben Brown, Erwin Frise and Gary Karpen laboratories. Please send comments or questions about the web site to BDGP atFRUITFLY dot ORG
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