The Zebrafish TPF and AGP server enables you
to access the current placements of clones on chromosomes.
What is a TPF?
A Tiling Path Format file specifies the order of clones along a larger molecule, e.g. chromosome. This order is based on all available mapping information, including restriction enzyme finger printing, marker placement, FISH etc. The file lists a minimal tiling path of clones out of all the clones mapped. You can view the map containing all clones using our FPC server.
The zebrafish tpfs are actively worked on, so change over time. The tpfs file displayed here include additional information to facilitate usability. The columns show
- the order of an element on the tpf
- the international clone name
- the Sanger project name
- the accession (if sequence is already available)
- the clone library
- the clone status within our sequencing pipeline
- the status date
The indicated gaps (type 3) are gaps in the physical map.
How can I get TPF data?
Select a chromosome or a chromosome subregion from the menu and click it. You will then get a display of this region's TPF data.
What is an AGP?
A Golden Path is a description of the assembly of an object, e.g. a chromosome, by listing all its components (clones) in order whilst specifying exact coordinates. It does not, however, describe the alignments between the components or give you any idea of the features on these components. For a detailed explanation of the format, please look here. Again, our format displayed here differs slighty from the standard to facilitate usability. The columns show
- the chromosome
- the start of the clone in chromosome coordinates
- the end of the clone in chromosome coordinates
- the rank of the entry
- the status (F = Finished, N = Not yet determined)
- the accession and version of the clone
- the start in clone coordinates
- the end in clone coordinates
- the strand in clone coordinates
Gaps are indicated by the status 'N', an arbitrary size and a type. 'Clone' specifies that a clone has been identified that will close this gaps but is not sequenced yet whereas 'contig' states a gap in the map.
How can I get AGP data?
When viewing a TPF, click on the red box in the upper right corner 'show AGP'. It will then show next to the TPF data. You can download sequence from contiguous regions by clicking on the green bars.