ARCHIVE
What's New on the NAGRP Animal Genome Web Site ( 2008 - 2013 )

Major updates / permanent additions:

  • NAGRP-8 species/bioinformatics coordinators information updated to reflect the renewed NAGRP coordination structure for the next 5 years
  • Update, Sep 25, 2013
  • What's new on the NAGRP animal genome web site (#3, 2013)
  • New, Aug 26, 2013
  • The new rainbow trout genome assembly is available on NAGRP data repository. The assembly was from 14,900 MTP clones/ 13,824 BACs in 1,152 pools that represent approximately 50X BAC sequence coverage. The sequences are also available for blast on the NAGRP blast server.
  • New, Aug 10, 2013
  • Do you have a software to share with the community (for free download)? The Animal Genomics Software Repository is ready for you to do so.
  • New, Aug 6, 2013
  • A new ANGENMAP FAQ item is added to explain why odd wobble characters occur on some angenmap posts and how to avoid them.
  • New, Jul 18, 2013
  • A mirror site in China for Animal QTLdb is set up to share the server load and for faster network speed for 18 Asian countries.
  • New, Jul 03, 2013
  • New Vertebrate Trait (VT) Ontology, Product Trait (PT) Ontology, and Clinical Measurement Ontology (CMO) web sites have been set up. This is a reflection of the recent new developments of the ATO into the three ontology projects.
  • Updated, Jun 28, 2013
  • A new threaded mails archive view is made available on the AnGenMap listserv to allow users browse mails by threads (by authors, by subject, by dates, etc). In addition, a web form is added to the listserv web view to allow reply posts or send new messages directly via web. This does not affect how current the users use the list with interactive emails.
  • Updated, Jun 20, 2013
  • Biomart on AnimalGenome.ORG is updated.
  • Updated, Jun 3, 2013
  • Search for candidate genes in QTLdb is made easier - Candidate genes is displayed where applicable when users search for traits or for partial gene names/symbols.
  • New, Jun 1, 2013
  • VCmap source code can now be downloaded for developers.
  • New, May 28, 2013
  • What's new on the NAGRP animal genome web site (#2, 2013)
  • New, Apr 24, 2013
  • Thanks to Paris Veltsos of the University of St Andrews, a copy of pre-compiled CRI-MAP for MacOSX platform is made available on the CRI-MAP Improvement web site.
  • New, Apr 21, 2013
  • Thanks to Bertrand Servin and coauthors of "High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly" (BMC Genomics 2012, 13:585) that provided 14,907 RH markers to serve as anchors between pig linkage/genome maps. This helps to improve the map resolution when transfer QTL to the latest pig genome build 10.2.
  • New, Apr 01, 2013
  • New usage on the NAGRP file-share platform: Upload your sequence file to request batch blast
  • New, Mar 08, 2013
  • New catfish RNA-Seq assembly data shared from John Liu group at Auburn University
  • New, Mar 07, 2013
  • A new function on AnGenMap - Mail Digest - is available
  • New, Mar 01, 2013
  • New addition to the Animal QTLdb data alliances is Data Citation Index (DCI) on the Web of Knowledge platform from Thomson Reuters. DCI provides a single point of access to quality research data from repositories across disciplines around the world
  • New, Feb 26, 2013
  • An Epigenetics Discussion Group mailing listserv and web site is set up
  • New, Feb 21, 2013
  • GBrowse is setup for CDS/mRNA predictions on 1670+ Oyster sequences
  • New, Feb 12, 2013
  • A new site for NRSP-8 community documents, reports and reach out
  • New, Jan 29, 2013
  • A mailing listserv and web site is set up for the OMIA Support Group
  • New, Jan 30, 2013
  • Annual reports, Newsletters, and NRSP-8 2014-2018 Rewrites are updated on Aquaculture, Cattle, Pig, Sheep, and Bioinformatics Coordination web sites
  • New, Jan 18, 2013
  • Updated chicken 60K SNP mapping data is available from Hans Cheng of ARS, USDA
  • New, Jan 16, 2013
  • What's new on the NAGRP animal genome web site (#1, 2013)
  • New, Jan 2, 2013
  • dbSNP "rs" and "ss" numbers for Pig 60K SNPs are available on the NAGRP Data Repository
  • New, Dec. 31, 2012
  • More data fields are added to the Animal QTLdb data download files (e.g. "test models", "significant levels", and "map types") so that users can sort them out on their own.
  • New, Nov 13, 2012
  • Made available is supplementary data for "Genome-Wide Association Study Implicates Testis-Sperm Specific FKBP6 as a Susceptibility Locus for Impaired Acrosome Reaction in Stallions" by Terje Raudsepp, Molly E. McCue, Pranab J. Das, et al. published on PLOS Genetics (PGENETICS-D-12-01716R1)
  • New, Nov 5, 2012
  • A GBrowse instance is set up to display sheep BACs and 50k SNPs genome alignments
  • New, Oct 26, 2012
  • VCMap Video Tutorials are online
  • New, Oct 14, 2012
  • The sheep genome assembly 3.1 data is made available in fasta and gff formats
  • New, Oct 09, 2012
  • The sheep genome assembly 3.1 is added to the NAGRP blast server for blast
  • New, Oct 09, 2012
  • A new version of the improved CRI-MAP software is available from Jill Maddox.
  • Update, Sep 13, 2012
  • Available OMIA gene alignments are added as new GBrowse tracks for cattle, chicken, horse, and pigs (Thanks to Dr. Frank Nicholas of The University of Sydney for providing the data)
  • New, Sep 12, 2012
  • What's new on the NAGRP animal genome web site (#3, 2012)
  • New, Aug 24, 2012
  • Several new information are posted on the Aquaculture Genome Projects web site
  • Update, Aug. 10, 2012
  • The 2013 PAG meeting hotel room share database is avilable to accept input now
  • Update, Aug. 7, 2012
  • QTLdb: Search for animal breeds associated QTLs is possible (experimenting)
  • New, Jul 9, 2012
  • VCmap (version 3.0) User's Manual is online
  • New, Jul 3, 2012
  • New pig build 10.2 annotations are ported to Biomart for downloads
  • Update, Jun 8, 2012
  • 4,730 human refseq sequences were blast mapped to pig build 10.2.
  • New, Jun 4, 2012
  • QTLdb: A QTLdb Curators Listserv List is set up to facilitate curators activities
  • New, June 1, 2012
  • QTLdb: Automated PubMed search now sents weekly notifications to all curators when new QTL publications are found
  • New, May 25, 2012
  • QTLdb: A new trait hierarchy navigator is available for users to browse for QTL
  • New, May 25, 2012
  • The developmental Pig Genome Database is open to public for trial use
  • New, May 16, 2012
  • Pig OligoArray elements are blast mapped to pig genome build 10.2
  • New, Apr 30, 2012
  • What's new on the NAGRP animal genome web site (#2, 2012)
  • New, Apr 23, 2012
  • New cattle 770k HD SNP and 64k SNP chip annotations are shared by James Koltes.
  • New, Mar 25, 2012
  • QTLdb: The QTL map locations conversion (cM to bp) algorithms is improved
  • Update, Mar 15, 2012
  • QTLdb: Users can now search multiple QTL for targeted alignments and meta-plots
  • New, Feb 28, 2012
  • The CRI-MAP Improvement Consortium web site "downloads" area is upgraded for users to upload and share their contributions.
  • New, Feb 21, 2012
  • A "SheepModels" listserv mailing list is set up
  • New, Feb 08, 2012
  • Affy array elements are blast mapped to pig genome build 10.2
  • New, Feb 02, 2012
  • Qinghua Nie (nqinghua@iastate.edu) posted a data file to share with the chicken genome community: Multisites_contigs_unigenes.xlsx
  • New, Feb 01, 2012
  • More defined search phrase can now be used for better targeted literature search within QTLdb
  • New, Feb 1, 2012
  • NRSP-8 Aquagenomics, Pig genomics, and Bioinformatics Coordination annual reports are posted. Check respective web pages for details.
  • New, Jan 16, 2012
  • Web site modified to reflect the change of NAGRP "Sheep" to "Sheep/Goat" Genome Coordination Program
  • New, Jan 15, 2012
  • QTLdb: QTL trait hierarchy browse are improved to allow better QTL data and reference overview by trait types as well as by traits
  • New, Jan 14, 2012
  • What's new on the NAGRP animal genome web site (#1, 2012)
  • New, Jan 05, 2012
  • New function added: easy reference list for all QTL within a chromosomal view window
  • New, Dec 18, 2011
  • Three more items in AnGenMap FAQ: How to write effective emails on AnGenMap, etc.
  • New, Dec 6, 2011
  • 770K ILumina HD SNPs structural genomics analysis data posted by James Reecy
  • New, Dec 2, 2011
  • AUGUSTUS pig gene predictions by Henrik Hornshoj et al are placed on GBrowse
  • New, Dec 1, 2011
  • Genome maps can be ported to QTLdb for Mbp map based QTL/eQTL/association (GWAS) data
  • New, Nov 28, 2011
  • ATO/QTL traits are now linked to VT/PT/CMO to stadardize the trait nomenclature
  • New, Nov 14, 2011
  • The cattle 770K High Density SNPs "rs/ss" dbSNP IDs are posted by Robert Schnabel.
  • New, Nov 6, 2011
  • Annotated cattle genes on UMD 3.1 is available on NAGRP site Biomart
  • New, Oct 30, 2011
  • New GBrowse tracks are added for 8.4M cattle SNPs and 3M chicken SNPs from dbSNP.
  • New, Oct 25, 2011
  • What's new on the NAGRP animal genome web site (#3, 2011)
  • New, Sep 23, 2011
  • New item in AnGenMap FAQ: platform to share non-plain-text files for AnGenMap emails.
  • New, Aug 31, 2011
  • SNPlotz: Horse 54k SNP chip data is added to the SNPlotz
  • Update, Aug 16, 2011
  • Horse GBrowse tracks are updated with 54k/74k SNPs, 3k RH and 10k STS markers data.
  • New, Jul 11, 2011
  • A developmental pig genome database is created; On-going progress are being made.
  • New, Jun 6, 2011
  • Experimental Biomart is setup on AnimalGenome.ORG to serve multiple species
  • New, May 19, 2011
  • The BEAP program is modified to assist users for easy setup. See its manual for details.
  • Update, May 11, 2011
  • The NAGRP data repository is expanded to host supplementary data for publications.
  • New, May 8, 2011
  • Updated pig genome assembly 10 is available for blast on NAGRP server
  • Update, Apr 28, 2011
  • What's new on the NAGRP animal genome web site (#2, 2011)
  • New, Apr 23, 2011
  • Cattle QTL alignment for UMD 3.1 build are available for download and visulization in GBrowse
  • New, Apr 21, 2011
  • New GBrowse track is added for the Chicken 60K SNP chip aligning with genes/QTL/etc
  • New, Apr 20, 2011
  • SNPlotz: Improved to allow user keep own upload files for customized plot/re-analysis
  • New, Apr 6, 2010
  • QTLdb chromosomal viewer is improved to include a list of traits for browsing
  • New, Mar 8, 2011
  • Expeditor tools are updated to meet the new Ensembl gene structure view
  • Update, Mar 2, 2011
  • Rainbow trout 2nd generation genetic map is updated with 1465 markers
  • Update, Feb 24, 2011
  • Aquaculture genome database links are updated
  • New, Feb 1, 2011
  • Catfish pseudo-chromosomes are on GBrowse
  • New, Jan 12, 2011
  • What's new on the NAGRP animal genome web site (#1, 2011)
  • New, Jan 10, 2011
  • A web form is set up to serve as a window to the Site Helpdesk
  • New, Jan 9, 2010
  • A platform for NAGRP members to share files individually or with the community
  • New, Jan 7, 2010
  • New SNP datatypes are added to the GFF Data Formattor tool
  • Updated, Dec 21, 2010
  • Pig genome preliminary assembly 9.2 is in the GBrowse to align with QTL and SNPs
  • New, Dec 15, 2010
  • Cattle UMD 3.1 assembly is included in the GBrowse
  • New, Dec 10, 2010
  • Cytogenetic G-banded chromosome ideogram are added to QTLdb maps for all species
  • New, Nov 16, 2010
  • QTL data are now exported also in BED format for download
  • New, Nov 4, 2010
  • Two QTL meta-plot tools are added to help users for their QTL meta-analysis.
  • New, Oct 31, 2010
  • NAGRP Data Repository for Community Members to Share Their Genome Analysis Data
  • New, Oct 23, 2010
  • Sheep QTLdb is set up, joining the the Animal QTLdb family with three more other species
  • New, Oct 01, 2010
  • What's new on NAGRP animal genome web site (#3, 2010)
  • New, Sep 27, 2010
  • Pig genome assembly 10 is released and available on the NAGRP bioinformatics blast server
  • New, Sep 22, 2010
  • Release 12 of the Animal QTLdb has been made public, with addition of 1,065 new QTL
  • Updated, Sep 13, 2010
  • Rainbow trout transcriptome characterized and put on NAGRP Blast Server
  • New, Jul 15, 2010
  • Blast Evaluate Pig Assembly 9b
  • New, May 30, 2010
  • The Animal QTLdb FAQ are updated to explain that the QTL_ID is stable
  • Updated, May 16, 2010
  • An improvement is made to the CateGOrizer to show the child GO:ids on each class
  • Update, May 6, 2010
  • What's new on NAGRP animal genome web site (#2, 2010)
  • New, Apr 27, 2010
  • Release 11 of the Animal QTLdb has been made public, with addition of 1,643 new QTL
  • Updated, Apr 23, 2010
  • The CateGOrizer is improved to better process very large data set
  • Update, Apr 7, 2010
  • Animal QTLdb frequently asked questions is updated with new items
  • Updated, Mar 23, 2010
  • QTL data are now exported also in SAM format for free download
  • New, Mar 5, 2010
  • GFF3 File formatter: A generic web tool to convert own mapping data into GFF3 format
  • New, Feb 20, 2010
  • QTL data link to NCBI Entrez Gene Database is automatically synchronized
  • New, Jan 30, 2010
  • What's new on NAGRP animal genome web site (#1, 2010)
  • New, Jan 04, 2009
  • Release 10 of the Animal QTLdb has been made public, with addition of 1,281 new QTL
  • Updated, Dec 30, 2009
  • Pig genome assembly v.9 on GBrowse: Sequenced BACs, Predicted genes, QTL, etc.
  • New, Dec 28, 2009
  • The current (developing) vertebrate trait ontology can now be viewed via AmiGO
  • New, Dec 11, 2009
  • SNPlotz: Improved for users to use Gensel or Illumina SNP IDs in their data set
  • Update, Nov 24, 2009
  • The CateGOrizer is improved to allow users to add their annotations to a data set
  • Update, Nov 2, 2009
  • Animal QTLdb: Mechanism is established to port data to NCBI Gene Database
  • New, Oct 22, 2009
  • Striped Bass Ovarian Transcriptome Sequence Contigs Database is set up
  • New, Oct 13, 2009
  • What's new on NAGRP animal genome web site (#3, 2009)
  • New, Sep 22, 2009
  • Animal QTLdb: Release 9 with significant more data added
  • Update, Sep 15, 2009
  • NEW: Virtual Comparative Map (VCMap): release #1
  • New, Aug 23, 2009
  • SNPlotz: A genome plot tool for SNP association studies
  • New, Jun 14, 2009
  • The rainbow trout 2nd generation genetic map is put on-line
  • New, May 30, 2009
  • The Cow Hits the News
  • New, Apr 24, 2009
  • What's new on NAGRP animal genome web site (#2, 2009)
  • New, Apr 20, 2009
  • NCBI horse genome information are ported to GBrowse for alignment display
  • New, Mar 31, 2009
  • Partial pig genome information from Sanger are updated into GBrowse
  • New, Mar 28, 2009
  • Bovine 50K SNP chip elements are aligned with cattle genome with GBrowse
  • New, Feb 27, 2009
  • Animal QTLdb data may be downloaded in .gff format for external analysis such as UCSC
  • New, Jan 31, 2009
  • What's new on NAGRP animal genome web site (#1, 2009)
  • New, Jan 06, 2009
  • QTLdb species main pages and FAQ page are updated to reflect recently added functions
  • New, Jan 06, 2009
  • Data download is made possible on Animal QTLdb
  • New, Dec 15, 2008
  • AmiGO is setup for Animal Trait Ontology browse and search
  • New, Nov 18, 2008
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