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AHPC

The Animal Health & Production Compendium

Changes to Compendia distribution data: the distribution tables, maps and references in datasheets have been restructured to handle the data better for updating and align with a geographic standard. Further details are available on the About page.

 

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Animal Genetic Resources

DAD-IS Domestic Animal Diversity Information System
FAO
DAD-IS is the Domestic Animal Diversity Information System hosted by FAO. It is a communication and information tool for implementing strategies for the management of animal genetic resources (AnGR). It provides the user with searchable databases of breed-related information and images, management tools, and a library of references, links and contacts of Regional and National Coordinators for the Management of Animal Genetic Resources. It provides countries with a secure means to control the entry, updating and accessing of their national data.

OMIA - On-line Mendelian Inheritance in Animals
University of Sydney
Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse, which have their own resources) authored by Professor Frank Nicholas of the University of Sydney, Australia, with help from many people over the years. The database contains textual information and references, as well as links to relevant PubMed and Gene records at the NCBI.

FunctSNP
CSIRO Livestock Industries
FunctSNP is a unified bioinformatics resource to link SNPs (as from genome-wide association or other post-genomic high-throughput analyses) with functional knowledge. Whilst there are many computational tools that support various aspects of genome-wide association studies, there is currently a need for bioinformatics solutions that facilitate the integration of data from multiple sources, particularly in animal genomics; FunctSNP is a database driven standalone tool that meets this need. It is comprised of an R package interfaced to custom built species-specific databases (for Cattle, Chicken, Sheep, Pigs and Human), which contain SNP data together with functional annotations extracted from online resources.

FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. Stephen J Goodswen, Cedric Gondro, Nathan S Watson-Haigh and Haja N Kadarmideen. BMC Bioinformatics 2010, 11:311.

dbAutoMaker
CSIRO Livestock Industries
dbAutoMaker is a suite of Perl scripts, which can be scheduled to run periodically to automatically create/update the customised SNP databases used by FunctSNP (see above).

PCIT
CSIRO Livestock Industries
PCIT is a tool to develop gene co-expression networks using high throughput microarray data based on data-driven soft thresholding to correlation matrices in order to identify meaningful pair-wise correlations. Automatic detection of a suitable parallel environment is used such that scripts are portable between parallel and non-parallel environments with no modification of the script. Whilst PCIT has been successfully applied to gene co-expression networks, it is general enough to be applied to any correlation matrix. To use PCIT you need to have R installed, and Rmpi if you wish to run PCIT in a parallel environment.

CRAN Package - PCIT
User Guide
Reference Manual
PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches. Nathan S. Watson-Haigh, Haja N. Kadarmideen and Antonio Reverter. Bioinformatics 2010, 26(3), 411-413.