You can find the legend for the colours here.

gEVAL/PGP Builds vary for each organism, however the GRC organisms are on a more frequent refresh cycle. For example, zebrafish builds are on a bi-monthly schedule.

1. gEVAL/PGP builds include unfinished sequence(phase 1 and 2 sequence) in the assembly, whereas the AGP viewers will substitute this with a gap place holder (certain assemblies include phase 2 but not phase 1).
2. gEVAL/PGP builds are more up to date because of the inclusion of unfinished sequences compared to AGP Viewers.

WGS assemblies represent full genome assemeblies using the whole genome shotgun approach. There are viewers for these assemblies for mouse and zebrafish. As well the data has been aligned to their respective gEVAL/PGP builds. Currently for GRC organisms, the wgs assemblies are primarily used to improve sequence content in regions not covered by clones but of course it is also useful for investigating potential sequence rearrangment and variation.

• Human, Mouse, Zebrafish - Genome Reference Consortium
• Pig - Sanger/Pig Sequencing Consortium
• Helminth - Sanger/Helminth Sequencing Group
• Rat - Rat Genome Sequencing Consortium

The gEVAL Browser is a frequently updated browser whose target audience is primarily directed to those who work on creating and improving assemblies. Commons examples of usage is to see what areas are, or should be targeted for sequencing, possible haplotypic variation and selection of new clones to sequence for a specific region. The gEVAL viewer while usually having a more updated path than Ensembl, is not a browser with a gene-centric focus. The fact there are cdna/transcript mappings, is more for using the model to compare neighboring clones its mapped on to.

Heres a check list to follow to see if 2 clones separated by a gap can be closed or not:

1. turn on the selfcomp track and see if there are reciprical alignments available for the two clones. If so and no overlap was generated then possible reasons are very high variation in the overlap, or one completely overlaps another creating what would be a false 5'/5' or 3'/3' join with the clone and the clone on the other end. If you do a alignment between the 2 clones and overlap is relatively acceptable, please let us know, and we either fix or let the appropriate people fix the issue.
2. turn on the end mapping track(s). First thing you want to do is look for spanning ends. These are the sequenced paired ends from the clone it came from. For example, a 123F01.T7 on clone A and 123F01.SP6 on clone B with correct orientation pointing towards the expected insert, can be chosen as a spanning clone. This clone can then be sequenced to fill that gap.
3. If there are no spanning ends, it could be possible that the gap is larger than a single clone, and some sort of walking out the edge may be required. An option is look for end hangers, these are ends that are on the edge of a clone to the gap with an orientation pointing towards the gap. Like a primer walk this clone can be sequenced added to the path, and the gap shortened.
4. Another option, if available is to use the wgs assemblies and see if any large wgs contigs cover a gap, if so no only will you possibly get an estimate of the gap size, but you can use the contig in combination with the clones on the edge to confidently choose hangers and spanners.
5. ** As always, regions of interest may be quite repetitve, and such a chosen hanger or spanner, may not be unique to be used. It is always useful to check the region with selfcomp, and if the end is not green colour, to see how repetitive the region the end hits is.

This is to say, how can I be sure that the clone or the region I am interested is where it supposed to be. Heres a couple strategies to confirm if this is the case or not.

• markers, although a genetic and physical map is a major resource for mapping work, as projects progress, more maps are generated and added, helping increase the resolution of the marker coverage across the genome. More contigs and clones can then be pinpointed. In the browser, the marker track can be turned on and the markers are colour coded. Magenta markers indicate the markers are where it should be on the chromosome, blue coloured markers indicate that it should not be on the current chromosome/location. See for more info.
• blue coloured end mappings, like markers, some ends based on fpc data, have a location associated with it. This too can be used like the markers, indicating whether or not the location is correct. See for more here.

The gEVAL browser will have builds of the tile path that is more frequent than that seen in Ensembl. This is because Ensembl will take a freeze of the path at one date and spend a bit of time preparing and completing numerous analysis that makes up its build. Because of this, Ensembl will have more analyses, specificaly gene-ctric ones. The gEVAL Browser is not fully intended to provide any analysis on genes or related data, it is more focused on sequence improvement of the available genomes. However having said that, if a gene of interest is in an poorly represented area in Ensembl, one can use the gEVAL browser to re-analyze the area, as a) the path will be more up to date containing finished and newly sequenced unfiniished clone sequence and b) the data and analysis will focus on giving an impression of the relative health of the region of interest. Navigation-wise it will be very similar to Ensembl as it uses a lot of its web framework. One addition in gEVAL browser is the use of Punchlists, specifically tailored list(s) that can be used to methodically resolve issues.

The GRC or Genome Reference Consortium is a group of educational institutes which was formed to improve the representation of reference genomes. At the time the human reference was initially described, it was clear that some regions were recalcitrant to closure with existing technology. The main reason for improving the reference assemblies are that they are the cornerstones upon which all whole genome studies are based (i.e. the 1000 Genomes Project).
The GRC currently maintains the reference genomes of human, mouse and zebrafish.

The members of the GRC are:

• The Wellcome Trust Sanger Institute
• The Genome Center at Washington University
• The European Bioinformatics Institute
• The National Center for Biotechnology Information

Human

library	external prefix	internal prefix	library size distribution	range used in gEVAL
Chori-17	CH17	bMO	link	146689-269814
Whitehead fosmid	WI2	fW	nolink	31067-48600
RPCI-11	RP11	bA	link	113124-228383
Chori-507	CH507	bPA	nolink	default
ABC7	ABC7	f7A	nolink	25492-49289
ABC8	ABC8	f8A	nolink	26065-46749
ABC9	ABC9	f9A	nolink	31855-47051
ABC10	ABC10	f10A	nolink	34984-46978
ABC11	ABC11	f11A	nolink	34406-45615
ABC12	ABC12	f12A	nolink	34762-44676
ABC13	ABC13	f13A	nolink	33534-44996
ABC14	ABC14	f14A	nolink	33137-46638
ABC16	ABC16	f16A	nolink	32107-43947
ABC24	ABC24	f24A	nolink	33193-44338
ABC27	ABC27	f27A	nolink	33265-44107

Mouse

library	external prefix	internal prefix	library size distribution	range used in gEVAL
RPCI-24	RP24	bN	L1L2	91404-242955
RPCI-23	RP23	bM	link	122253-270705
Whitehead mouse fosmid	WI1	fM	nolink	28450-50967
Chori-25	CH25	bMS	link	43595-162830
Chori-36	CH36	bML	link	113292-247285

Zebrafish

library	external prefix	internal prefix	library size distribution	range used in gEVAL
CHORI-211	CH211	zC	link	97784-232694
DanioKey	DKEY	zK	nolink	87399-268251
DanioKey Pilot	DKEYP	zKp	nolink	121938-239280
CHORI-73	CH73	zH	link	67324-152296
RPCI-71	RP71	bZ	link	90017-205409
ZFISHFOS	ZFISHFOS	zF	nolink	32722-49432
CHORI-1073 (FOS)	CH1073	zFD	nolink	31911-45771

Pig

library	external prefix	internal prefix
PigE	PigE	bT
CHORI-242	CH242	bE
SBAB bI Clones	PigI	bI
WTSI_1005	WTSI_1005	fSS

Depending on organism, gEVAL still takes a freeze of the tiling path for each build roughly on a 2-4 month cycle. Clones that may be seen as being sequenced, or unfinished, may have progressed if you were to look at it today. To see the current status of all the clones and the path itself, the Sanger Institute made tool Chromoview can be used for Human, Mouse, Zebrafish and Pig. It is updated twice weekly and will display clone paths per chromosome for each organism, the overlaps, the AGPs and links to EMBL records and to the gEVAL.