NAGRP Bioinfo - What's New

ARCHIVE What's New on the NAGRP Animal Genome Web Site ( 2013 - 2018 )
Major updates / permanent additions:
A set of cattle genome variant mapping data (to ARS-UCD1.2 Cow Genome Assembly, by Robert Schnabel group from the University of Missouri) is deposite to the NAGRP Community Data Repository.		Update, Sep. 12, 2018
Aquaculture genomics newsletter #47 is distributed and deposited.		New, Sep. 10, 2018
A new version (LBO version 3.6) of Livestock Breed Ontology data is loaded.		Update, Sep. 6, 2018
FAANG Funded Projects list is updated. Six newly funded projects are added. Congratulations to the new grant recipients!		Update, Aug 31, 2018
What's new on the NAGRP animal genome web site (#3, 2018)		New, Aug 23, 2018
Cattle QTL/association data are now lifted to the new ARS-UCD1.2 genome build. A new feature with this update is that dynamic hyper links are enabled for each alignment to link to Animal QTLdb for details.		New, Aug 10, 2018
Thanks to Robert Schnabel from the University of Missouri, with his efforts mapping the cattle SNPs to the new genome build ARS_UCD1.2, we were able to lift the cattle QTL/association data to the new build. A preliminary set of cattle QTL/association data based on build ARS_UCD1.2 is now available for download on Animal QTLdb. Please check it out and let us know if you identify any problems. (NOTE: Due to the limitations of the number of genomes we can handle within the current Animal QTLdb, cattle QTL/association data for the new build is not available for web tools, such as web browse. We are making efforts to improve for handling a wishful number of genome builds.)		New, Jul 27, 2018
A new version of Vertebrate Trait (VT) Ontology data is made public.		Update, Jul 11, 2018
A new version of Livestock Product Trait (LPT) Ontology data is made public.		Update, Jul 2, 2018
Annotations for the new cattle genome assembly ARS_UCD1.2 are loaded to NAGRP Jbrowse alignment tool. The alignment tool is ready to accept any new alignment information for display when they become available. Cattle QTL/association tracks will be added once we get the new SNP mapping information.		New, Jun 06, 2018
An improvement is made to the NAGRP Community Data Repository to allow restricted access to data (available upon request only). With this controlled access to data, we aim at providing more flexibility for data owners in terms of how, when. and to whom certain data can be made available while meet the requirements for publications.		New, May 08, 2018
A frequently asked questions and answers section has been added to the CorrDB. This is to address common questions raised with regard to the design, usage, application, utilities, new developments, and other related issues in the development of the CorrDB.		New, May 03, 2018
What's new on the NAGRP animal genome web site (#2, 2018)		New, Apr 29, 2018
In response to some community requests, we have created HISAT2 indexes for the most recent genome builds of cattle, chicken, horse, pigs, and sheep and made them available through the NAGRP Data Repository. The HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads. Based on the HISAT and Bowtie2 implementations, HISAT2 aligns reads in SAM format, which can be used by any tool that uses SAM format, for example, SAMtools, GATK, etc.		New, Apr. 26, 2018
The NRSP-8 annual reports from aquaculture, bioinformatics, cattle, horse, poultry, sheep/goat, and swine coordinators are online. Also came online are a work summary of NRSP-8 accomplishments during 2013-2018, a proposal for the next 5 years (2019-2023), and an updated list of current NRSP-8 community leaders.		New, Apr. 6, 2018
A total of 1,645 cattle transcription factors (TFs), including 865 sequence-specific DNA-binding bovine TFs and 780 putative transcription cofactors (TcFs) derived from known interactions with the identified TFs, are added to NAGRP Jbrowse tracks to align with QTL/association data among other genomic features on the bovine genome, thanks to Marcela Maria de Souza, Luciana Correia de Almeida Regitano, et al from Brazil for providing the data from their recent studies A comprehensive manually-curated Compendium of Bovine Transcription Factors.		New, Mar. 28, 2018
The Animal QTLdb has introduced using DOI (Digital Object Identifier System) on data that has a DOI record. This is to facilitatethe link-out service useful for unification of records identifications and database federations. Where applicable, DOI will become part of required data for sending data to the Animal QTLdb.		New, Feb. 24, 2018
To solve platform dependency problems, a virtual machine (VM) was set up to host the Virtual Comparative Map (VCmap) Visualization Tool (see project info for more information). Please update your bookmark, or URL link, from the old: "https://www.animalgenome.org/VCmap" to the current: "http://vcmap.animalgenome.org".		New, Feb. 12, 2018
Video records for the two recent meetings, Genome2Phenome: to update the USDA blueprint and Livestock HTP and Big Data, are put online. These meetings were to discuss new challenges in animal genomics in terms of big data and genome technologies, and to develop meaningful and tangible goals for the next decade for the NAGRP efforts.		New, Jan. 26, 2018
What's new on the NAGRP animal genome web site (#1, 2018)		New, Jan 3, 2018
The new pig genome build version 11.1 is now supported by the Animal QTLdb.		New, Dec 18, 2017
The curator tools has been developed for the Animal Correlation Database (CorrDB) and ready to accept free registration by anyone who wish to be a CorrDB curator to enter own or public correlation and heritability data.		New, Dec 6, 2017
As part of the Animal QTLdb/CorrDB co-development efforts, functions are developed to link QTL data with trait correlation data through common trait terms where such data exist. For example, within the CorrDB, under the Table View of correlation data, a hyper-linked red "QTL" label is added when QTL data exists on the trait; Like-wise, within the QTLdb on the trait search results, an hyper-linked tag is added on traits where correlation data are found.		New, Nov 6, 2017
"AnGenMap Frequenly Asked Questions" has been updated to address several confusing problems mostly seen by new users.		Updated, Oct 6, 2017
A "Frequently Asked Questions" page is being developed for the NAGRP Community Data Repository platform.		New, Oct 2, 2017
The Animal QTLdb has a new feature: a "gene centric view" and a "trait centric view" of QTL/association data where underlining gene information is available. This helps users to relatively quickly to interrogate and understand genotype-to-phenotype information in a synopsis. A quick way to use the tool to view information is to try a search by genes or by traits (e.g. try "grand search", then go to "genes" or "traits"), or go from a "Trait Details" view to following links on "List all QTL/association data where a gene may exist". The returned query results are displayed in one of the two ways - "gene centric" or "trait centric" view - at user's choice.		New, Sep 17, 2017
The NAGRP Data Repository is undergoing another round of restructuring by setting up new data areas for each aquaculture species. The current data area "aquaculture" is planned to deprecate, while existing data in this area are being moved to their respective species areas. The data moved will be also kept available in their current "aquaculture" area until March 1, 2018. As part of the move, data areas for "catfish" and "rainbow trout" have been set up with data inherited from "aquaculture" area.		New, Sep 07, 2017
What's new on the NAGRP animal genome web site (#3, 2017)		New, Aug 29, 2017
The NAGRP Data Repository for publication supplementary data files has been restructured with: (1) addition of customized file description area to allow authors to better reflect what are hosted (optional; in addition to what they can put in their publications); This was made retrospectively compatible for 10+ publications having custom file descriptions. (2) modification of the web interface for supplementary data uploads for better collection of meta-data when initiating the data host process; (3) addition of a new machanism to allow only reviewers to access a set of deposited data while the data is considered confidential prior to publication (i.e. public access to the data is not possible during the review period, or until authors give a green light to lift the restriction).		New, Aug 10, 2017
The web services on https://www.AnimalGenome.ORG is now completely served by a SSL implemented web server, after 5 months test run period during which both HTTP and HTTPS visits were served. Now all traffic to the HTTP protocol (http://www.AnimalGenome.ORG) is now automatically forwarded to HTTPS server.		New, Aug 3, 2017
The web site for the Functional Annotation of ANimal Genomes (FAANG) consortium, https://www.faang.org, is now operated on a Secure Sockets Layer (SSL) implemented web server.		New, Aug 1, 2017
A "permanent record locator" is implemented on the AnimalQTLdb to provide unique and stable links to all curated QTL/association data on a publication. The new "permanent record locator" is a replacement of an "URL Link" function introduced two years ago to overcome some of its shortcomings. It can be used by the authors to refer to their published data, to provide proof of evidence of data entry at the Animal QTLdb to journal editors/manuscript reviewers, and to serve other purposes. All QTLdb curators/editors have access to this tool for their curated data.		New, Jun 14, 2017
The new NCBI pig genome annotation data for the assembly build version 11.1 is made available at the NAGRP shared data repository.		New, Jun 1, 2017
A web site to sign an open letter to call for Restoration of NIFA/AFRI Foundational Program: Support the Animal Breeding, Genetics and Genomics Research is set up for signature and comments.		New, May 26, 2017
What's new on the NAGRP animal genome web site (#2, 2017)		New, Apr 28, 2017
The Secure Sockets Layer (SSL) is implemented on https://www.AnimalGenome.ORG web server for encrypted data transfer from/to the server.		New, Mar 27, 2017
The new pig genome assembly build version 11.1 is installed on the NAGRP Blast server, for blast searches, available on both blastn and megablast engines. The genome sequence is also available for download from the NAGRP/Pig data repository. Annotations to this build is not yet available.		New, Mar 10, 2017
Selected NCBI and Ensembl video tutorials on how to use their sites/tools are summarized for user's covenience.		New, Feb 19, 2017
An online tool is made to batch match Illuminar SNP names to rs numbers.		New, Feb 14, 2017
A Wordle representation of QTL/association-mapped traits by years can be found in the data summary area of each species on the Animal QTLdb.		New, Jan 10, 2017
What's new on the NAGRP animal genome web site (#1, 2017)		New, Jan 11, 2017
The Animal QTLdb curation tools are improved to allow automatic verification and streamlined curation of SNP information as part of the QTL/association annotations. The improvements involved data quality control processes in which multiple genome builds are maintained for cattle, chicken, and sheep.		New, Dec 21, 2016
The hosted publication supplementary data is now merged with NAGRP Shared Data Repository. Its contents can be found by searching the data repository.		Update, Dec 14, 2016
The Animal QTLdb curation protocols are modified that preliminary SNPs (with 'ss' numbers only) are allowed to be entered to anchor QTL/association mapping locations. The QTL/association mapping data represented by the 'ss' SNPs are subject to normal data release procedure while the 'ss' SNP information will eventually be replaced with their 'rs' SNP information once the 'rs' numbers are assigned by dbSNP.		New, Nov 08, 2016
The AnGenMap listserv moderator's switchbox was improved to include functions to aid list moderator's reviewing and posting jobs. These included functions/tools to clean mail text mixed with quoted-printables, and to decode MIME coded text.		New, Oct 25, 2016
Thanks to Ben Rosen from the USDA/ARS and his colleagues for their efforts putting together a new goat genome assembly. The new goat assembly is now loaded to JBrowse for map alignment views. Currently added tracks include NCBI gene model annotations and NCBI gene structure Gnomon.		New, Oct 5, 2016
Room share bulletin board for PAG, PAG-Asia and other meetings are improved by adding several administrator tools and a security layer to prevent robot-like hackers.		Update, Sep 15, 2016
What's new on the NAGRP animal genome web site (#3, 2016)		New, Aug 31, 2016
Introducing the new chicken genome build (GG_5.0) to the QTLdb. We have completed the first trial of lifting the QTL/association coordinates to the new build. Continued efforts will be made to verify the transferred data in the upcoming weeks. Please note the availability of chicken QTL/association data for download and for graphic visualization online may be affected.		Update, Aug 28, 2016
The AnimalGenome.ORG site is being moved to a new server with more computing powers which will help us to meet new challenges. The move of multiple services (more than a couple dozen hosted web sites, databases, virtual domains, etc). The complete migration of the services and development platform has been going with relatively smoothly and expected to complete in the next couple months.		Update, Aug 2, 2016
We have engaged with EBI (EMBL European Bioinformatics Institute) for collaborative VCF file archives. At EBI/EVA (European Variation Archive) all VCF data will be validated to to enter their archive repository, and further streamed to NCBI/dbSNP. See NAGRP VCF Data Repository for updates in the coming months.		New, Jul 30, 2016
File formate examples are being added to the "Minimum information required for Animal QTLdb data entry" page in the form of Excel work sheets. Click the icon on the right hand side to see an example, and scroll to the bottom of the page to download all Excel templates . More such templates are still being added to provide a convenient way for users to prepare their data for entering into the QTLdb.		Update, May 26, 2016
What's new on the NAGRP animal genome web site (#2, 2016)		New, Apr 30, 2016
The WebApollo were revived on a dedicated NAGRP virtual machine platform as part of the efforts to develop cyber resources for the Striped Bass Genome project led by Benjamin Reading and Charles Opperman at the North Carolina State University.		Update, Mar 6, 2016
TOM-connectivity related cattle genes: 137,887,921 connectivities among 16,608 probe sets representing 11,125 genes. TOM-connectivity is measured by weighted correlation network analysis on the GEO archive data using "Topological Overlap Measure (TOM)" ( Langfelder P, Horvath S: WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics 2008, 9:559) to find "related" genes.		New, Feb 24, 2016
EpiDB goes online. The development of EpiDB is a collaboration with James Koltes of University of Arkansas to provide gene and epigenetics expression data useful for dissecting quantitative trait data in livestock.		New, Feb 04, 2016
We have set up a private data share area for Dr. Zhou's group at University of California-Davis on the NAGRP Data Repository. This provides a model for individual NRSP-8 labs to have their data share utilizaing the NAGRP bioinformatics platform.		New, Jan 21, 2016
The Animal QTLdb was present at PAG 2016 Booth on the Plant and Animal Genome XXIV in San Diego, Jan 9-10, 2016.		New, Jan 9, 2016
What's new on the NAGRP animal genome web site (#1, 2016)		New, Jan 04, 2016
A new plot tool for whole-genome view of QTL/association data was created. This is to overcome the space limitations of the current plot tool. To use it, start from browing by traits, click on a "link out" icon by a trait name to go to "Find all QTL for this trait type" will do.		New, Dec 22, 2015
Working with Dr. Frank Nicholas and Matthew Hobbs of Sydney University, we are in a process to migrate the Online Mendelian Inheritance in Animals from it original Sydney University site to Iowa State University (http://OMIA.AnimalGenome.ORG). We expect the full migration will be completed in the coming months.		New, Dec 3, 2015
We have been developing a livestock breed ontology (LBO) which was started with its utilities in Animal QTLdb. A most recent copy of the LBO is deposited in Bioportal.ORG, and also made available through AmiGO hosted on AnimalGenome.ORG.		New, Dec 1, 2015
We have recently developed a number of web modules to support the research activities of the FAANG community in terms of structured working groups, grant application oriented collaborations and communications. The same functions/tools can be applied to other groups if such interests exist.		New, Nov 16, 2015
The Animal QTLdb now can accept user inputs to improve the quality, and add values to the QTLdb data content. The types of user inputs may include additional annotations, comments, or report problems.		New, Oct 29, 2015
The Animal QTLdb has rolled out new information pages on minimum information required and steps needed to upload large quantity of new QTL/association data.		New, Oct 20, 2015
Video recorded sessions of GO-FAANG are put onine. The GO-FAANG was held October 7-8, 2015 at the US National Academy of Sciences Building in Washington, DC		New, Oct 14, 2015
A Jbrowse and a WebApollo were up running on a dedicated NAGRP virtual machine platform as part of the efforts to develop cyber resources for the Striped Bass Genome project led by Benjamin Reading and Charles Opperman at the North Carolina State University.		New, Sep 15, 2015
What's new on the NAGRP animal genome web site (#3, 2015)		New, Aug 31, 2015
User interface for NAGRP File Sharing Platform is improved for easy use.		Update, Aug 17, 2015
New items are added to the AnGenMap FAQ: who can post recruitment advertisements and why? Now the FAQ has 32 items.		New, Jul 24, 2015
A new pre-compiled CRI-MAP (version 2.5.07) for MacOSX-10.10.4 is made available by Jill Maddox from Australia.		New, Jul 22, 2015
A horse genotype VCF file is shared by Mohammed Al Abri (Cornell University) and Samantha Brooks (University of Florida). See the NAGRP VCF File Repository for details		New, Jul 06, 2015
New horse genotype data are shared by Jessica Petersen from the University of Nebraska-Lincoln and Mohammed Al Abri from Cornell University. Jessica's data is part of their recent publication "The American Quarter Horse: Population structure and relationship to the Thoroughbred" on Journal of Heredity. (2014) 105:148-162.		New, Jun 26, 2015
What's new on the NAGRP animal genome web site (#2, 2015)		New, Apr 28, 2015
A new version of CRI-MAP is made available by Jill Madox on the CRI-MAP Improvement web site. The main change in this version pertains to the implementation of a version of parallelisation using forks and pipes for the get_likelihoods function. This means that flips, all and build will use multiple cpus when more than one order is being tested.		New, Apr 16, 2015
Support for OMIA continues -- A virtual machine site is set up for hosting OMIA. The site has a new URL: http://omia.animalgenome.org		New, Mar 12, 2015
The NAGRP Data Share Repository now has over 1000 files for sharing. A new search function is implemented in the data repository site to help users quickly narrow down the area for targeted files s/he is looking for.		New, Feb 7, 2015
GenomeWeb interviewed with Jim Reecy: NAGRP Bioinformatics Arm Seeks Input from Livestock Genomics Community to Set Future Priorities.		New, Feb 5, 2015
A new web site is set up for the international consortium on Functional Annotation of Animal Genomes (FAANG), a.k.a. http://www.faang.org, which supports the collaborative efforts with wiki sites, member forums, communications for working committees. All project related information can also be found on the site.		New, Jan 8, 2015
What's new on the NAGRP animal genome web site (#1, 2015)		New, Jan 6, 2015
A preliminary application programming interface (API) platform (developing) has been added to the Animal QTLdb		New, Dec 30, 2014
A dedicated virtual machine platform is setup to develop cyber resources for the Striped Bass Genome Database (http://stripedbass.animalgenome.org/), a project led by Benjamin Reading and Charles Opperman at the North Carolina State University.		New, Dec 15, 2014
Horse QTL data is now streamed to UCSC Genome Browser for alignment display and data mining using the tools available at UCSC.		New, Nov 05, 2014
The NAGRP VCF Data Repository is actively used. The most recent additions are eight (8) VCF files from Drs. Ottmar Distl, Joern Wrede (Institute of Animal Breeding and Genetics, Hannover), Dr. Ludovic Orlando (University of Copenhagen, Centre for GeoGenetics), and Dr. Danika Bannasch (University of California Davis).. Thanks to Dr. Carrie Finno from University of California-Davis to help facilitating with this.		New, Oct 25, 2014
The state of art online alignment tool - Jbrowse - has been setup for QTL/association data alignment with annotated genes among other genome features. The advantage of Jbrowse is that it allows easy user quantitative data - XYPlot, Density, in BAM or VCF format - to be loaded for comparisons directly to users browser in users local environment.		New, Oct 3, 2014
QTL/Association discovery trends - a Wordle representation (experimenting...)		New, Sep 19, 2014
What's new on the NAGRP animal genome web site (#3, 2014)		New, Sep 2, 2014
The complete implementation of livestock animal QTL tracks at the UCSC site took extended time and they are finally made available in the recent new release of UCSC Genome browser.		New, Aug 3, 2014
A horse genotype VCF file is shared from Claire Wade (University of Sydney) and Jessica Petersen (University of Nebraska-Lincoln). See the NAGRP VCF Data Repository for details		New, Jul 12, 2014
A video tutorial is made available on workarounds to a VCmap menu dysfunction on MacOS platform		New, Jul 10, 2014
We have begun to create video tutorials to introduce new tools developed for Animal QTLdb users to easily access and analyse the QTL data curated into the database. More tutorials are to be added in the coming weeks.		New, Jun 30, 2014
Thanks to Jeremy Walker [JWalker@neogen.com] the pig 70K SNP chip annotations are now available from the NAGRP data repository		New, Jun 10, 2014
A new search tool is added to the Animal QTLdb to allow query of neighboring QTL/associations by a user-defined view window. Its utility comes with a sliding window, also defined by user on viewing size and slide distance. The tool also included a graphical representation of the two window positions relative to their chromosome locations. Hyper links enable users to bring the QTL/associations to visualize for their alignments in GBrowse.		New, May 27, 2014
A new QTLdb curator tool is added to help users batch deposit their QTL/association data.		New, May 22, 2014
The latest releases of NCBI genome annotations within the last 12 months for several livestock species (cattle: 2013-08-06; chicken: 2013-06-19; pig: 2013-09-29; horse: 2013-09-23) have been made available through the NAGRP shared data repository (look for "Genome_annotations" sub-folder in respective species folders). Information are also linked from each NAGRP species home pages.		Update, May 16, 2014
The CateGOrizer is now bundled with a new external tool, Revigo, for the convenience of users to take CateGOrizer outputs directly to Revigo for a semantic representative subset analysis.		Update, May 16, 2014
What's new on the NAGRP animal genome web site (#2, 2014)		New, Apr 21, 2014
Two annotation data sets in '.bed' format are made available by Heather Holl and Samantha Brooks from Cornell University to share with the horse genomics community. The data sets are on a de novo assembly of three lamellar transcriptomes. Alignment was performed to EquCab2 using BLAT and has been repeats filtered.		New, Apr 11, 2014
An user contributed FAQ item is added to the Animal QTLdb FAQ list thanks to Shangang Jia. This user kindly shared his experience how to transfer QTL location coordinatyes from the current genome build to an older version using LiftOver. This FAQ also listed a few other similar tools for the same task.		New, Apr 5, 2014
The Animal QTLdb is improved to include pleiotropic QTL/association data. The pleiotropy data can be accessed through data summaries of a publication. i.e. go to details of a publication (abstract), then click on "List QTL" links, as shown in this example.		New, Mar 31, 2014
The Animal QTLdb is improved to allow users analyze the QTL by their trait types (i.e. "feed intake" has included "average daily feed intake", "days on feed", "dry matter intake", and "residual feed intake"). To use it, browse the trait hierarchy to find trait of your interests, click on its linkout icon () to "find all QTL on this trait type". This brings up a genome view of all chromosomes showing all mapped QTL in the genome. When there are more QTL on a chromosome than the available space could hold, a "more" link will show to bring you to that particular chromosome in order to display all QTL of the trait type on that chromosome. Currently this function is implemented only in Cattle QTLdb. Stay tuned...		New, Mar 22, 2014
The Animal QTLdb map view is improved to allow users to view QTL of user's choice on a chromosome for alignment display. To do so, first come up with a list of QTL IDs from your data mining process, then copy all QTL IDs into the "Search" box on a QTLdb chromosome view page, then click "go".		New, Mar 18, 2014
The NAGRP VCF File Repository (beta version) is open to public to accept file deposits. This platform is designed for collaborative VCF file storage, handling, information abstraction, querying, and data re-use. See our poster at the 2014 PAG for details: VCF Miner: A Platform and Tools for Collaborative Information Mining from Next-Generation Sequence Variant Data.		New, Mar 10, 2014
Search for Vertebrate Trait (VT) Ontology, Product Trait (PT) Ontology, and Clinical Measurement Ontology (CMO) within the Animal QTLdb is made possible. Use the current search tool "Find if your trait has a QTL" or "Grand search" to start. On the results page, VT/PT/CMO are now shown where mapped. Note on this page there are new choices on the top search box to limit the search "In VT/PT/CMO traits" or "all". e.g. when "In VT/PT/CMO traits" is checked, the results will be limited to, AND grouped by, VT/PT/CMO traits only. - In addition, if any QTL for the trait exists in "other" species, it is also listed, for exploration of the same trait into a different species. Another way to start the search is from respective VT/PT/CMO project home pages, by the heading "Utility: Animal QTLdb", click expansion arrow to open a search box.		New, Feb 21, 2014
Thanks to Brian Dalrymple, Sean McWilliam, and James Kijas of CSIRO for providing sheep STS marker mapping information, now we have made available the genome coordinate estimates of sheep QTL/association data. Check the sheep QTLdb to find more.		New, Feb 07, 2014
Vertibrate Trait (VT), Production Trait (PT), and Clinical Measurement Trait (CMO) terms are included on QTLdb searches. See QTLdb trait search to try it out.		New, Feb 06, 2014
Several Ensembl functional annotated SNP chip data sets are made available via NAGRP Data Repository. These include Ensembl VEP annotated bovine high density (770K) SNP data, bovine low density (6K) SNP data, 50K SNP chip data, chicken 600K SNP chip data, horse 50K SNP chip data, and pig 60K SNP chip data (Thanks to James Koltes for forwarding the information)		New, Jan 18, 2014
Frustrated by too many Animal QTLdb search options/tools to choose from? Now there is a "grand search" tool available to simplify the database-wide search for you. The searched results are linked to each specialized search tools for you to explore further. Find it on the top of each species page, as well as the "Search Tools" pages.		New, Jan 08, 2014
What's new on the NAGRP animal genome web site (#1, 2014)		New, Jan 06, 2014
Animal QTLdb is expanded to include horse for QTL/association data collections.		New, Dec 15, 2013
Animal QTLdb Search Tools page is reformated for users to easily locate a data search tool for information, for exploration, or for data analysis.		Update, Nov 18, 2013
A new tool is added to the Animal QTLdb -- which allows users to search for traits of interests for their location distributions throughout the genome. Go to "Search", under "Data Analysis Tools", look for item "Find QTL genome distributions on a particular trait".		New, Nov 15, 2013
New SNP genotype analysis/process scripts from Guangtu Gao, et al. are added to the NAGRP Tools repository		New, Nov 12, 2013
New rainbow trout SNP data from publication by Yniv Palti, Guangtu Gao, et al. is added to aquaculture genomics data repository		New, Nov 12, 2013
A new tool is added to the Animal QTLdb -- for species that has a genome build (currently cattle, chicken, and pig), users now can search and download QTL data by their genome locations (in terms of "bp"). Go to "Search", under "Data Analysis Tools", look for item "Find QTL by their genome locations" to try it out.		Update, Oct 22, 2013
Animal QTLdb data is synchronized to Ensembl. Users can now utilize Ensembl genome viewer for gene feature/phenotype variation aliagnments. Choose a species where its genome is available (e.g. cattle, chicken, sheep, or pig) and search for traits of your interests to find more.		New, Oct 10, 2013
NAGRP-8 species/bioinformatics coordinators information updated to reflect the renewed NAGRP coordination structure for the next 5 years.		Update, Sep 25, 2013

Major updates / permanent additions: