Roslin Bioinformatics - ArkDB
ArkDB is a generic, species-independent database built to capture the state of published information on genome mapping in a given species. It stores details of references, markers and loci and genetic linkage and cytogenetic maps which can be drawn using the online map-drawing application. Data from linkage maps held within the ArkDB system can be drawn alongside their corresponding genome sequence maps (extracted from ENSEMBL).
You may also be interested in the standalone map-drawing application ArkMAP, which uses the same underlying codebase as the ArkDB system.
ePCR maps of ArkDB Markers on Ensembl Assemblies
Where possible we have used the EMBOSS primersearch program to map the primer pairs of ArkDB PCR based markers to genome assemblies provided by Ensembl. Multiple hits and hits to non-assembled fragments and contigs were discarded, and the remaining unique ePCR mapping positions have been entered into ArkDB system as ePCR sequence maps for each chromosome (for Pig, Cow, Chicken and Turkey) with a different map provided for each genome assembly present in ENSEMBL.
- Chicken build Galgal4 (Ensembl71)
- Pig build Ssc10.2 (Ensembl67)
- Cow build UMD3.1 (Ensembl66)
- Turkey build Turkey_2.01 (Ensembl66)
- Chicken build WASHUC2 (Ensembl53)
- Cow build Btau4.0 (Ensembl54)
- Pig build Ssc9 (Ensembl56)
- Turkey build UMD2.0 (Ensembl57)
These GFF files can be used as external datasources toload the ArkDB mappings into the Ensembl Browser. (To display the GFF files in Ensembl follow the menu: 'Configure this page' -> tab:'Custom Data' -> menu:'Attach Remote File').
The genome assembly used for each ePCR analysis is noted along with the relevant release of Ensembl. The genome builds used by each Ensembl release are recorded at Ensembl. For example Ensembl releases 50 to 63 all used the Btau4.0 assembly, so that the GFF mapping file Cow build Btau4.0 should correspond to Cattle coordinates in each of those releases.