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Showing results for: [ Genomics ]
In the absence of detailed functional annotation for any livestock genome, we used comparative genomics to predict ovine regulatory elements using human data. Reciprocal liftOver was used to predict t... morehe ovine genome location of ENCODE promoters and enhancers, along with 12 chromatin states built using 127 diverse epigenome.
Here we make available the following files:
a) Sheep_epigenome_predicted_features.tar.gz: contains the final reciprocal best alignment from ENCODE proximal as well as chromHMM ROADMAP features. The result of reciprocal liftOver.
b) liftOver_sheep_temporary_files.tar.gz: We have
added a new tar file with liftOver temporary files
i) LiftOver temporary files mapping human to sheep,
ii) LiftOver temporary files mapping sheep back to human and
iii) Dictionary files containing the link between human to sheep coordinates for exact best-reciprocal files.
OCE Post Doc - Conseq Animal Domesticati - - Published 09 Nov 2017
This data set contains the genomes of Helicoverpa armigera and Helicoverpa zea and the relevant annotations.
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution an... mored divergence of two highly polyphagous and invasive Helicoverpa pest species
Legacy data - Insect genomics - Published 11 Aug 2017
Example input files suitable for analysis by Eagle. The data were obtained from a large genome-wide association study (GWAS) performed in outbred mice and published on the Heterogeneous Stock Mouse we... moreb site. The data were reorganized to make it suitable for input into Eagle.
Acquired - Mouse Genome-wide Association Study Data - Published 24 May 2017
Draft genome assemblies of 380 Bradyrhizobium isolates collected from soil samples at the base of Acacia acuminata trees in Southwest Australia
Biodiversity Eco Know & Serv - Awards & - Survey of rhizobia in soils of South-West Australia - Published 03 Mar 2017
Reproduction and recruitment underlie the maintenance of biological communities. For most marine organisms the ocean environment provides the potential for widespread dispersal of organisms during var... moreious life cycle stages via currents, tides and wind.
Within the Kimberley region, key biological communities have a range of reproductive modes. Understanding patterns of larval connectivity is critical to managing the exposure of biological communities to disturbances in space and time.
KSN Project 1.1.3 employed genomic tools (microsatellite DNA markers and single nucleotide polymorphisms) and microchemistry to provide the first comprehensive measurements of the distances moved by marine organisms between Kimberley reefs, and how frequently organisms move between the Kimberley and other regions (e.g. offshore shoals, the Pilbara). The research also identified potential barriers to movement. Seven organisms (two
hard corals, two seagrasses, a mollusc, two fishes) were chosen as models for exploring connectivity in the Kimberley at both fine and broad scales.
This metadata record applies to three of the seven species investigated as part of project WAMSI 2 KSN 1.1.3. The data held is Raw SNP genotype. Metadata records associated with other species and lodged by AIMS, WA Museum, Curtin University, Department of Fisheries (WA) and Edith Cowan University can be accessed via Pawsey.
WAMSI-Kim 1.1.3 Ecological connectivity - Survey - Published 05 Dec 2016
Files associated with this project:
== MiSeq PE and Mitochrondrial reads ==
== HiSeq PE Data ==
= Mitochondrial genome =
... more- A_hancockii_mito_complete.fa (complete mitochrondrial genome)
= Nuclear genome =
- FRR3425_A_hancockii_noMITO_min_200.fasta (contigs > 200bp)
- FRR3425_A_hancockii_noMITO_belowCutoff_200.fasta (contigs < 200bp)
**Gene Calls (AUGUSTUS)**
- FRR3425.outfile (GFF)
- FRR3425.outfile.aa (Amino acid calls for genes)
- FRR3425.outfile.cdexons (Exons)
- FRR3425.outfile.codingseq (Coding seqs)
Legacy data - Fungal genomics - Published 07 Mar 2017
A collection of raw and analysed sequence resources across several Hieracium species and genotypes related to the study of apomixis. This collection was generated by the Asexual Seed Formation researc... moreh team in CSIRO led by Anna Koltunow.
This data collection supports the publication : Generation of an integrated Hieracium genomic and transcriptome resource enables exploration of small RNA pathways during apomixis initiation
David S. Rabiger, Jennifer M. Taylor, Andrew Spriggs, Melanie L. Hand, Steven T. Henderson, Susan D. Johnson, Karsten Oelkers1, Maria Hrmova, Keisuke Saito, Go Suzuki, Yasuhiko Mukai, Bernard J. Carroll and Anna M.G. Koltunow*
BMC Biology 2016
OCE, PDF, KOL014-RAB018, Switching betwe - Development and Characterisation of Hieracium Genomics Resource - Published 28 Apr 2017
The DEW pipeline is a one command line solution that aligns reads, corrects expression biases (eXpress), TMM normalizes (edgeR) and produces FPKM values that are then visualized with pretty ggplot gra... morephics.
This BZ2-compressed tar archive provides the software and licensing statements. DEW is written in Perl and requires a SQLite database and is supported for Linux 64-bit computers. The homepage of the software can be found at http://dew.sourceforge.net.less
Cont to TCP01 Dissecting Adaptive - transcriptomics software development - Published 06 Jan 2015
Whether working on a model or non-model species for biomedical, economical or evolutionary research, next-generation sequencing has enabled biologists to rapidly generate a reference sequence for down... morestream applications and hypotheses generation. With the exception of a limited number of species, functional annotation is conducted by in-silico experiments based on sequence similarity. Some groups are also enriching their data with expression studies. JAMp is a platform that allows biologists to reclaim the analysis of transcript reconstruction experiments by providing an automated process for generating functional annotations and a user-friendly overview of these in-silico experiments. The entire software is built so that novice command-line users can take a transcriptome assembly and generate websites like those found in our demo.
Cont to TCP01 Dissecting Adaptive - genome annotation software development - Published 06 Jan 2015
An increased number of genomes are being made public but few individual research are willing to take ownership of their own data. Indeed, the current model is for genome sequences to be handled by seq... moreuencing centers or large bioinformatic repositories (RefSeq or Ensembl). Even though using these widely used and standardized repositories and center is an excellent model to decrease the cost of completing a genome project, this comes at a cost. First, these groups have in-house pipelines built and customized for the projects that financially support them (i.e. small genomes of microbial human pathogens and largely fully complete genomes such as Drosophila or human) rather than say a highly polymorphic species from a natural ecosystem. Second, the lack of a robust funding model means that these repositories are do not have the resources to offer community-wide support and customization of a pipeline. Third, and perhaps most importantly, these centers and repositories usually lack the domain expertise associated with the biology of the species.
For these (and perhaps others?) reasons, genome consortia that have access to genomicists (or PhD students and post-docs willing to learn) are either collaborating with bioinformatic laboratories or investing in their own annotation capability. This endeveavour has been greatly helped by the public availability of the tools used by the repositories and sequencing centers (e.g. GMOD, Ensembl and sequencing-center specific platforms such as those from the Broad Institute). The GMOD project specifically specializes in compact, user friendly solutions that just_work. For example, MAKER requires a few minutes of configuration to deliver a standardized annotation for gene models. At the other side of the spectrum, Ensembl delivers a comprehensive solution, database and informatic pipelines that - in the hands of a highly-trained bioinformatician - can deliver the same depth and level of annotation as that used by the EBI. There really is no a solution that fits in-between. There is also almost no software that also wishes to educate the user rather than offering a black box. Finally, there is no solution that we know of that can also functionally annotate the genome (a la BLAST2GO but free) and then link the concept of gene model (feature) annotation with functional annotation.
The JAMg software was created to address the issue of creating gene models (feature annotation) and was built by Alexie Papanicolaou at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) with some brilliant support from Brian Haas at the Broad Institute. The software and manual are written so that to guide the annotation process so that users can follow the process closely. Even though with JAMg you will not need another genome annotation pipeline, JAMg does not aim to replace other genome annotation pipelines (e.g. each sequencing center has its own): it does aim to support nascent genome annotators and (ultimately) educate its users about genome annotation in general. As part of our Just_Annotate series, JAMg links with JAMp and WebApollo to provide a first solution for users wishing to go from genome assembly to deriving biological hypotheses.
This BZ2-compressed tar archive provides the software, HTML documentation and licensing statements. The expanded folder tree requires at least 2.5 GB of disk space. JAMg software is written in Perl and is supported for Linux 64-bit computers. See the homepage at http://jamg.sourceforge.net for new versions.
Supplementary data for the BMC Genomics paper titled: "Identification and Characterization of Three Chemosensory Receptor Families in the Cotton Bollworm Helicoverpa armigera"
Catalytic Dissecting Adaptive Potential - Phlyogenetics analysis - Published 05 Jun 2014
Genomic information for Bacillus pumilus 'Fairview' including: all contigs Velvet split by base pair size.
1218.1 MECSM Phase 2 - Survey of microbiology in coal seam gas reservoirs - Published 10 Mar 2014
Genomic information for Cairneyella variabilis including:
- All protein calls from AUGUSTUS 2.6.1 (generated 24-10-2013)
- cdsexons calls from AUGUSTUS 2.6.1 (generated 24-10-2013)
- coding sequence ... morecalls for proteins from AUGUSTUS 2.6.1 (generated 24-10-2013)
- all contigs less than 1000 bp from Velvet
- all proteins with signal peptides from SignalP
- mitochondrial genome
Legacy data - Fungal genomics - Published 18 Sep 2014
The collection contains SNP genotypes from a diverse collection of the world’s sheep breeds. For each breed, a selection of sheep (20 – 100) were genotyped using the ovine SNP50 BeadChip. Following qu... moreality filtering, the final dataset contains 49,034 SNP genotyped from 2819 animals. Genotypes are made available in .PED and .MAP format ready for analysis in programs such as PLINK. To assist users with interpretation, a help file is included describing the data format along with additional information.less
CLSD 1206.1 NextGenBreedOpt C2012/5905 - SNP genotyping - Published 06 May 2013
The collection contains the genome sequence of a diverse collection of sheep. For each animal, sequence reads are available to a depth of approximately 10 fold genome coverage. Sequence reads are made... more available in BAM format. Sequence polymorphisms are made available in VCF format following comparison of each animal’s sequence to the sheep reference genome assembly (v3.1). To assist users with interpretation of the collection, the reference genome (FA format) and genome feature files (GFF3 format) are included for viewing using software such as the Integrative Genome Viewer (IGV).less
CLSD 1206.1 NextGenBreedOpt C2012/5905 - Genome sequencing - Published 22 Jul 2013
The Australian National Wildlife Collection is a significant biodiversity resource aiding the study, classification and documentation of Australia’s terrestrial vertebrates (excluding fresh water fish... more) . In April 1976, it was formally recognised by its gazettal as the Australian National Wildlife Collection by the Commonwealth Government.
The Australian National Wildlife Collection holds approximately 200 000 irreplaceable scientific specimens, including skins, skeletons, specimens in spirit, bird eggs, tissues and a wildlife sound library. The collection focuses on terrestrial vertebrates of Australia and Papua New Guinea and rodents of South-East Asia. There are also specimens from other parts of the world.
ANWC research addresses the diversity, evolution, and conservation of Australia's wildlife, focussing on its systematics and taxonomy (study of evolutionary relationships among organisms) and biogeography.less
Australian National Wildlife Collection - Biological Specimen Collections - Published 30 Jan 2013