Zebrafish genome Resources Workshop
Zebrafish Genome Resources - One-Day Workshop - Tuesday 5th July
In association with the 7th European Zebrafish Meeting, the Wellcome Trust Sanger Institute and ZFIN are pleased to announce a one day "Working with Zebrafish Genome Resources" Workshop on the 5th of July 2011 in Edinburgh.
The Open Door Workshop provides an introduction to bioinformatics tools freely available on the internet, focussing primarily on Zebrafish Genome data. The workshop features hands-on training in the use of public databases and web-based sequence analysis tools, and is taught by experienced instructors from the Wellcome Trust Sanger Institute and ZFIN. Applications are now open, more information can be found here.
Registration is now open. There will be a course fee of £35 for all participants. Participants will be expected to arrange and fund their own travel and accommodation.
Please send your enquiries to zebrafish-odw@sanger.ac.uk.
New Ensembl gene build
A new zebrafish gene set has been built and released in Ensembl 61. This gene set now for the first time includes the previously separate RNAseq gene models and also the gene models derived from the manual annotation, previously only available in Vega. Details about the process can be found here.
Zv9 released in Ensembl e60
The new zebrafish genome assembly Zv9 has been released in Ensembl e60. This release includes a new gene build, using a modified Ensembl pipeline that now - for the first time - uses RNASeq gene models to refine the gene set traditionally built based on protein and cDNA evidence. The final gene set comprises 24,020 protein-coding genes and 38 genes that have been identified as pseudogenes.
New Vega release
A new zebrafish Vega database has just been released. It contains 16,410 manually annotated genes on 11,261 finished clones.
OpenDoor Workshop 2011 registration open
In association with the 7th European Zebrafish Meeting and the Wellcome Trust Sanger Institute, we are pleased to announce a one day "Working with Zebrafish Genome Resources" Workshop on Tuesday 5th July 2011. Registration is now open.
Zebrafish Genome joins GRC
After the release of the integrated zebrafish genome assembly Zv9 by the Wellcome Trust Sanger Institute, the genome sequence has now been handed over to the Genome Reference Consortium (GRC) for continued maintenance and further improvements. The GRC is currently working on replacing whole genome shotgun sequence with high quality finished clone sequence, closing remaining gaps and placing yet unlocalized sequence. More details can be found here.
assembly Zv9 released
The Sanger Institute has released the 9th integrated zebrafish genome assembly, Zv9, in pre-ensembl. For this assembly, the clone contigs have been placed and oriented using the new high-density meiotic map SATMAP. Remaining gaps in the clone path were filled with sequence from a new whole genome shotgun assembly WGS31 that was created by combining Illumina and Capillary reads from double-haploid Tuebingen individuals. More Information on the assembly can be found here.
OpenDoorWorkshop 2010 material available
Tutorials and talks from the OpenDoorWorkshop 2010 'Working with Zebrafish Genome Resources' are now available.
RNAseq gene models in Ensembl 58
Ensembl release 58 contains a new set of gene models using Illumina RNAseq data from 9 zebrafish tissues and developmental stages. Fragmented polyA+ RNA was paired end sequenced to read lengths of 37, 54 or 76 bases at the Wellcome Trust Sanger Institute as part of the Zebrafish Transcriptome Sequencing Project, European Read Archive ERP000016. Gene models have been automatically produced as described in Ensembl documentation. More information can be found in the Ensembl documentation and the Ensembl Blog.
One-day workshop on Zebrafish Genome Resources
In association with the 9th International Meeting on Zebrafish Development and Genetics and the Wellcome Trust Sanger Institute, we are pleased to announce a one day "Working with Zebrafish Genome Resources" Workshop (The workshop will run from 09:00 - 16:30). More information here, you can enrol here.
A new Vega database has been released on the 17th of December. It contains 15,761 manually annotated genes on 10,755 finished clones.
New Vega Release
A new Vega database has been released on the 30th of March. It contains 14,707 manually annotated genes on 8,954 finished clones.
Zebrafish Open Door Workshop at Rome conference 2009
Applications are now open for this workshop to be held at Palzzo di Congressi, Rome, Italy; in conjunction with 6th European Zebrafish Genetics & Development Meeting (15th July 2009). Click here to register.
New Vega released
A new Vega database has been released on the 18th of December. It contains 13,596 manually annotated genes on 8,954 finished clones.
You can now use the community annotation tool to comment on the Zv8 assembly. Your comments are visible via a DAS track in the Zv8 pre-ensembl and will help us improving the assembly process.
assembly Zv8 released
The Sanger Institute has released the 8th integrated zebrafish genome assembly, Zv8, in pre-ensembl. This assembly features a sigificantly improved placement of clone and WGS components. Information on the assembly can be found here.
Chromoview clone path browser
The new chromoview features the live clone paths of all species sequenced at the Sanger Institute, including zebrafish. You can search for clones with their accession or name, browse the paths and download the sequences. Chromoview replaces the previously used tpf/agp browser and offers much more functionality.
new tile path browser
The tile path browser allows you to view the latest tile path files of every zebrafish chromosome including subregions (haplotypic variants) and contigs from the AB strain. Using the 'show agp' button you can find out about the exact coordinates of overlaps and download sequence. More detailed explanations can be found here.
WebFPC database update
The WebFPC database has been updated. This database displays the latest zebrafish physical map and allows searching and browsing for clones in contigs.
Vega Release
The Sanger Institute has released a Vega update on the 27th of September 2007. It contains more than 11,100 manually annotated genes on over 415 Mb of annotated sequence.
Zv7 released in Ensembl
The Sanger Institute has released the seventh zebrafish genome assembly, Zv7, in Ensembl. The database features repeatmasking, marker placement, alignments with cDNAs, ESTs and peptides, mapped BAC ends, expression patterns, as well as comparative genomics data and data mining tools. The gene build resulted in 21,322 genes, 98 pseudogenes and 4,053 non-coding genes. Please note that previous Ensembl data built on assembly Zv6 are still available in the Ensembl archives.
Zebrafish assembly Zv7 and Pre Ensembl released
The seventh zebrafish assembly, Zv7, has been released today. You can download the genome sequence from our FTP site. We have also released an extended Pre Ensembl database where you can browse the sequence and gene set.
The Sanger Institute has released an update of the Danio rerio Vega database on the 12th of July 2007. It contains nearly 10,400 genes on over 370 Mb of annotated sequence.
The Sanger Institute has released an update of the Danio rerio Vega database on the 16th of May 2007. It contains nearly 9500 genes on over 330 Mb of annotated sequence. Of these, 573 are located on 'haplotype scaffolds', regions thought to be from haplotypes different to that in the reference assembly
ZF Models Workshop 2007
The ZF Models workshop 2007 will take place from the 23rd until the 29th of April 2007 at the Wellcome Trust Sanger Institute in Cambridge. This workshop is aimed at researchers at all levels and will focus on the use of web resources that have been developed in conjunction with the Zebrafish Genome Sequencing Project. We shall include lectures on a variety of topics, e.g. mapping the zebrafish genome, sequencing techniques and sequence analyses, as well as hands-on exercises to explore bioinformatics resources via the web and via self-written perl scripts. For an agenda and registration information please go here.
The Sanger Institute has released an update of the Danio rerio Vega database on the 21st of December, 2006. It features 6,569 finished clones. 1,854 full clones and additional single loci with ZFIN record have been manually annotated resulting in 6,958 genes so far. Clone sequencing and manual annotation are still ongoing and the progress will be reflected in future releases.
The Sanger Institute has released an update of the Danio rerio Vega database on the 16th of October, 2006. It features 6,357 finished clones. 1,874 clones mainly on chromosomes 4,5,18,19,20 and 22 have been manually annotated resulting in 5,950 genes. Clone sequencing and manual annotation are still ongoing and the progress will be reflected in future releases.
New genebuild on zebrafish assembly Zv6
An updated gene set has been generated for the Zv6 assembly. As in the previous genebuild, transcripts were generated based on protein evidence and clustered in genes; these genes were then assigned names based on alignment to known entries in public databases, with ZFIN names being given priority. In addition, a new zebrafish expression patterns database has been added to Mart.
Frequent Web FPC releases
The WebFPC database has been updated again and will now be updated every month. This database displays the latest zebrafish physical map and allows searching and browsing for clones in contigs.
gene DAS tracks
You might have noticed that you can make Vega genes visible in Ensembl now and vice versa using DAS tracks. In order to switch Vega genes on in Ensembl, go to 'DAS sources' and check 'Vega Transcripts' (example). To see Ensembl genes in Vega, check 'Ensembl Transcripts' (example). Please note that this only includes genes that were annotated in Vega so far on clones that are present in both databases. We are currently working on transferring also genes that are e.g. in Zv6 scaffolds.
The WebFPC database has been updated. It allows searching and browsing for clones in contigs in the physical map. more info
Zv6 released in Ensembl
The Sanger Institute has released the sixth zebrafish genome assembly Zv6 in Ensembl. The database features repeatmasking, marker placement, alignments with cDNAs, ESTs and peptides, mapped BAC ends, expression patterns, microarray and ZF-Models data as well as comparative genomics data. The gene build resulted in 21,503 genes, 130 pseudogenes and 3,421 non-coding genes. Please note that the previous Ensembl data built on assembly Zv5 are still available in the Ensembl archives.
The Sanger Institute has released an update of the Danio rerio Vega database on the 13th of June, 2006. It features 6,210 finished clones. 2,080 clones mainly on chromosomes 4,5,18,19,20 and 22 have been manually annotated resulting in 5,684 genes. Clone sequencing and manual annotation are still ongoing and the progress will be reflected in future releases.
Vega release
A new Danio rerio Vega database has been release on the 8th of May, 2006. It comprises 5,922 finished clones. The clones on chromosomes 4, 18,19,20 and 22 (1,794 in total) have already been manually annotated resulting in 4,815 genes. Clone sequencing and manual annotation are still ongoing and the progress will be reflected in future releases.
Zebrafish assembly Zv6 and pre-ensembl released
The sixth zebrafish assembly Zv6 has been released today. You can download the genome sequence from our ftp site. We have also released a Pre-Ensembl database where you can browse the sequence together with alignments from different sources. Please note that these preliminary databases don't feature a gene build. Subsequent annotations including the Ensembl genebuild are ongoing and will be added as soon as they are completed.
ZF-Models meeting in Leiden
The zebrafish resources tutorial has been made available in an updated form for the annual ZF-Models workshop in Leiden.
ZFIN expression patterns mapped to Zv5
The expression pattern data curated by ZFIN has been mapped to the Zv5 assembly. The data is visible as a feature track in Ensembl ContigView and as a 'Similarity matches' entry in GeneView.
Zv5 released in Ensembl
We are pleased to announce the release of a new Ensembl database based on the zebrafish assembly Zv5. This release features a gene build that produced 22,877 Ensembl genes with 32,143 transcripts. Please note that Zv5 has now replaced the Zv4 assembly. The Ensembl build for Zv4 is accessible from the Archive Ensembl sites. This new release introduces a new look and feel for the Ensembl site with a major redesign of the underlying code. Most of the dynamic pages (eg ContigView, GeneView) have only minor cosmetic changes , in addition to the new template and stylesheets, some links have been moved from the body of the view to the new side-bar.
Zebrafish Genome Resources Workshop
The Sanger Institute, ZFIN and NCBI organise the "Zebrafish Genome Resources Workshop" to be held concurrenlty with the 4th European Zebrafish Meeting in Dresden (Germany) on the 14th and 15th of July 2005.
Zebrafish assembly Zv5 and pre-ensembl released
The fifth zebrafish assembly Zv5 has been released today. You can download the genome sequence from our ftp site. We have also released a Pre-Ensembl database where you can browse the sequence together with alignments from different sources. Please note that these preliminary databases don't feature a gene build. Subsequent annotations including the Ensembl genebuild are ongoing and will be added as soon as they are completed.
new zebrafish vega release
A new zebrafish vega database has been released. It contains 4,544 clones on chromosomal tiling paths, 1,108 of which have been manually annotated resulting in 4,457 gene transcripts. Most of the additions in this release are from the annotation of chromosome 18. The ContigView pages include a new track 'Assembly Tags' that highlights various features relevant to the quality/status of the finished sequence. You can find the database at http://vega.sanger.ac.uk/Danio_rerio.
A new zebrafish vega database has been released. It contains 4313 clones on chromosomal tiling paths, 865 of which have been manually annotated and revealed 3682 gene transcripts.
A new Vega database has been released. It contains 3945 clones with 2345 manually annotated genes. This Vega release now enables you to view Ensembl genes with the finished clones that are contained in both the current Ensembl and Vega databases. In order to make them visible, please select them under 'DAS tracks' on contigview pages. You can also enable the display of Vega genes in appropriate clones in Ensembl in the same way.
A new vega database has been released. It contains 3453 clones with 1807 manually annotated genes.
change to fpc database
The zebrafish fpc map, released via WebFPC on the 19th September 2004, uses externally recognised clone names in the display e.g. DKEY-110K5, instead of internal Sanger Institute clone names e.g. zK110K5. In order to ease any problems the transition may cause, the existing version of WebFPC will remain in place until November the 1st and additionally the clone search will continue to accept searches for clones in either naming format.
Ensembl 1-day courses at your institute
Ensembl has two full time help-desk scientists who answer questions posted to the helpdesk. In addition they have developed a quite extensive 1-day course suitable for up to 30 people with a hands-on training aspect in Ensembl. They regularly give this course to researchers in academic institutions worldwide.
You can download a pdf file with further information here.
new Zv4 mapsearch database
In order to alleviate locating markers in the Zv4 assembly, mapped ESTs and BAC ends, a new mapsearch database was released.
new Zv4 ensembl
We are pleased to announce the release a new ensembl version based on the zebrafish assembly version 4 (Zv4). This new database features a gene build that produced 23,524 ensembl genes with 32,062 transcripts. Please note that Zv4 now has replaced the Zv3 assembly. This means that Zv3 is no longer available as a web browser, but you can still download Zv3 data.
Madison 2004 tutorials
The Madison 2004 tutorials from NCBI, ZFIN and Sanger can be downloaded now. The Sanger part is available in a browsable from here.
Fluorescence In Situ Hybridisation
In collaboration with Dr. Charles Lee at Brigham and Women's Hospital, Boston, and with the Sanger Cytogenetics group we have begun to place contigs onto the genome using Fluorescent In Situ Hybridisation (FISH) on metaphase spreads of chromosomes derived from embryo tissue. We hope to define chromosomal locations for many of the unplaced contigs this way. Gap sizes between anchored contigs can be determined using fibre FISH. An improving view of the cytogenetics of the Zebrafish will enable more accurate chromosome sizing and identification.
New Zebrafish Vega database
A new zebrafish vega database has been released. It contains 2786 clones on chromosomal tiling paths.
zebrafish assembly Zv4 released
The fourth zebrafish genome assembly Zv4 has been released today. You can download the genome sequence from our ftp server and browse/search/download it pre-ensembl.
Zv4 pre-ensembl
A Zv4 pre-ensembl has been released today. The full ensembl database including a gene build is scheduled for release in September 2004.
FPC database modification
The FPC database will undergo a noteworthy change with the next version (to be released in 2-3 weeks). We have re-numbered the FPC contigs with the aim of simplifing our merging process. With the next release we will provide a conversion file listing the old contig and new contig number for each clone. As with previous versions the contig numbers will continue to change as the database develops, it is therefore advisable to use clone names/accessions to follow particular regions/sequences.
two computer biologists wanted
We have two positions available to work on the ZF models project. For details please check the job advertisement and the ZF-models homepage.
ensembl news
From today onwards, the ensembl releases are based on a different way of storing the sequence. You will see this on the contigview pages, they don't display names like ctg30.1, ctg30.2, etc. anymore. Instead this will all be ctg30, but if you move your mouse over the sequence, it will offer you to export either the whole supercontig or just the current 'chunk', e.g. what used to be ctg30.2. The new ensembl release also features translated BLAT comparisons to the human genome now ('HS trans BLAT' under 'compara' option on contigview).
Zv2 data wanted?
In case you're interested in Zv2 data and haven't saved them in time before the Zv3 ensembl was released: You can still access the old Zv2 ensembl data dumps.
mapping data
The Zv3 data is now searchable in mapsearch. You can search a certain supercontig for all associated mapping data (ESTs and STSs with mapping information and also BAC ends) or search for the placement of a certain marker in Zv3.
Zv3 ensembl released
The new Zv3 ensembl database features a gene build comprising 22409 genes.
Zv3 pre-ensembl
A Zv3 pre-ensembl has been released today. It comprises the sequence of the first zebrafish assembly that could be tied to the fpc map. The full ensembl database including a gene build is scheduled for release in February 2004.
zebrafish assembly Zv3 released
The third zebrafish WGS assembly Zv3 has been released today. This is the first assembly that could be largely tied to the fpc map. You can download the genome sequence from our ftp server and browse/search/download it pre-ensembl.
Second assembly Zv2 of the zebrafish genome released
The new zebrafish ensembl database has been released. This database is using the WGS assembly Zv2 and features an ensembl gene build.
Zebrafish Vega database
The manually annotated clones from the clone sequencing project are now browsable in the newly released vega database.
Zv2 Assembly Mapping
We mapped sequenced BAC ends, STSs and also ESTs with linkage group information to the new assembly Zv2. You can search for the markers on assembly contigs, or for the contigs that contain a certain marker.
New zebrafish whole genome shotgun assembly Zv2
The new zebrafish whole genome shotgun assembly Zv2 is available today. The data can be searched using both SSAHA and BLAST and downloaded from the ftp site. Please read the assembly information page.
Pre-Ensembl Zebrafish database
A pre-ensembl database has been build on the new zebrafish whole genome shotgun assembly Zv2. It features initial annotations like repeat masking, ab initio gene predictions, Blast searches against protein, cDNA and EST databases and marker placement with MarkerEPCR.
The assembly couldn't be tied to a map, therefore comes in 83470 individual non-connected supercontigs. For internal reasons these were randomly put together into 363 assembly chunks of a size of roughly 5Mb. A gap of 5kb was inserted in between each neighbouring supercontig to make them distinguishable. Please look out for these 5kb gaps and don't assume that sequence on either side belongs together.
Genome Monitoring Table
The zebrafish genome has been added to the Genome Monitoring Table.
Zebrafish Ensembl database 7.08.3 released
The new zebrafish ensembl database 7.08.3 has been released. Please note that it is based on clone sequences, not on the new assembly.
Zebrafish genome assembly is available
The Zebrafish genome assembly is available today. This data can be searched at Ensembl using both SSAHA and Blast. Data can be downloaded from the ftp site. more
Zebrafish BAC end sequences
The BAC end sequences from the mapping project have been submitted to dbGSS.
RepeatMasker
The online RepeatMasker now accepts multiple fasta entries and also lists of accession numbers.
Also you can mask your sequences with the help of our zebrafish RepeatMasker web server using a library of more than 1000 repeats.
The first zebrafish Ensembl database
The first zebrafish Ensembl database based on unfinished and finished clone sequences from a datafreeze in January 2002 was released on 25th March 2002.
Zebrafish DAS Server
A DAS server is available based on the first zebrafish Ensembl database (which itself is soon to be published).
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Last Modified Tue Mar 27 14:34:28 2007
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